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View Code? Open in Web Editor NEWMISO: Mixture of Isoforms model for RNA-Seq isoform quantitation
Home Page: http://genes.mit.edu/burgelab/miso/index.html
MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation
Home Page: http://genes.mit.edu/burgelab/miso/index.html
MISO (Mixture of Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. By modeling the generative process by which reads are produced from isoforms in RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform. MISO uses the inferred assignment of reads to isoforms to quantitate the abundances of the underlying set of alternative mRNA isoforms. Confidence intervals over estimates can be obtained, which quantify the reliability of the estimates. Please see http://hollywood.mit.edu/burgelab/miso/ for MISO manual and documentation. *Note: MISO is no longer maintained. This repository is left for archival purposes.*
Guidelines on Python packages installation
Filtering out reads that
That identifies:
Add argument to Sashimi plot to only plot junctions that have at least N
reads if given:
... --min-junctions N
And back. Use the functions in GFF.py.
Fix Python version path issue. Automatically retrieve correct Python path within run_events_analysis
.
Trivial change to hypothesis_test.py
: allow sample comparison between two samples that were running using different no. iterations/burn-in/lag parameters, i.e. make no assumptions about how many MCMC samples were produced.
Add sanitized GFF annotations for events. Also offer annotations with introns. Reorganize annotations into systematic categories on separate page in manual and link to it. Clearly separate exon-centric and isoform-centric annotations.
Handle BAM files that have no CIGAR string (i.e. are unaligned)
Automatically. Consider read pairs that match a subset of the isoforms with a unique fragment length (within some reasonable limits).
Hi,
I'm running Miso on Mac OS X 10.8.3 and am having frequent errors of this sort:
Python(57341) malloc: *** error for object 0x104120d00: incorrect checksum for freed object - object was probably modified after being freed.
I am running the --compute-genes-from-file step and looking at alternative splicing events.
Thanks
Pre-filter reads (with bedtoools) to select events to run on, to save time wasted looking through events that don't meet the coverage criteria
Hello,
When I attempt to use run_events_analysis.py
, I get the error:
MISO (Mixture of Isoforms model)
run_events_analysis.py interface is deprecated. Please run 'miso' instead.
But there are no examples or documentation on http://genes.mit.edu/burgelab/miso/docs/. Please add some instructions on how to run standalone miso
.
Thanks,
Olga
More aggressive error checking for procedures calling tagBam
and processing its output
Hi,
I'm trying to compute the insert length distribution given a constitutive exons file.
The bam file comes from TopHat, but misopy is complaining that there are no read pairs, though Flagstat claims otherwise. I tried --no-bam-filter but it made no difference.
I have checked the fastq files & the pairs have the same IDs except of course 1 for R1 & 2 for R2.
Any help would be greatly appreciated. This is my command & error output. Thanks ali
python misopy/pe_utils.py --no-bam-filter --compute-insert-len tophat2.mm10.bam misopy-0.4.6/exons/Mus_musculus.NCBIM37.65.min_1000.const_exons.gff --output-dir /misopy-0.4.6/insert-dist/
Computing insert length distribution of 1 files:
tophat2.mm10.bam
In the method "count_isoform_assignments" in the file "reads_utils.py" if one of the transcripts has not been assigned a read then it is never returned with 0 value and eventually is missed in the output column "assigned_counts".
eg consider a gene with 4 transcripts of which only the first 2 are assigned reads. In this case transcirpts 3 and 4 are never returned by the method.
Potentially use zlib
or arcode
. At best a ~3 fold reduction in total file size. Consider concatenating multiple event files from same batch.
scipy
still too difficult for most users to install. Replace all KDE-related code and other statistical code that uses scipy.stats
with numpy
-based alternative.
Hi Yarden,
I have subscribed to the mail list but there is still no confirmation so I ask the question here.
MISO run_miso.py --compare-samples perform pairwise comparison. If I have replicate on the samples, what is the best strategy to combine the results?
Marco
Hi,
Can Miso compare more than one WT/control to more than one Mutant/knockdown?
This would be really useful
Thanks alig
i think your code is great
Hello Yarden et al,
This is more of a feature request than a bug.
I'm trying to understand the ID scheme of the provided gff3 files. It says in the documentation as an example, that the ID of one SE entry was "arbitrarily" chosen to be the coordinates of the 5' upstream exon, the SE itself, and its 3' downstream exon. However, I don't see this in the current SE.hg19.gff3 file:
(obot_virtualenv)[obotvinnik@tscc-login2 prettyplotlib]$ grep exon ~/genomes/miso_annotations/hg19/SE.hg19.gff3 | head
chr1 SE exon 16854 17055 . - . ID=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.A.dn;Parent=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.A;gid=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-
chr1 SE exon 17233 17742 . - . ID=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.A.se;Parent=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.A;gid=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-
chr1 SE exon 17915 18061 . - . ID=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.A.up;Parent=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.A;gid=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-
chr1 SE exon 16854 17055 . - . ID=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.B.dn;Parent=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.B;gid=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-
chr1 SE exon 17915 18061 . - . ID=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.B.up;Parent=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.B;gid=chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-
chr1 SE exon 17233 17368 . - . ID=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.A.dn;Parent=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.A;gid=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-
chr1 SE exon 17606 17742 . - . ID=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.A.se;Parent=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.A;gid=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-
chr1 SE exon 17915 18061 . - . ID=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.A.up;Parent=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.A;gid=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-
chr1 SE exon 17233 17368 . - . ID=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.B.dn;Parent=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.B;gid=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-
chr1 SE exon 17915 18061 . - . ID=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.B.up;Parent=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-.B;gid=chr1:7778:7924:-@chr1:7469:7605:-@chr1:7096:7231:-
For example, the first exon is on the negative strand and has a start
and stop
of 16854
and 17055
. However, its ID is chr1:7778:7924:-@chr1:7096:7605:-@chr1:6717:6918:-.A.dn
, which doesn't include either of those numbers!
This has been especially confusing when attempting to interpret MISO output, and going to the middle chromosome location in the ID, and finding no reads there. But the location specified by the start
and stop
columns in the original .gff3
file are correct, (which is comforting) but it's kind of a pain to have to grep for this arbitrary ID every time.
Is it possible for these .gff3
files to be updated such that the ID matches the chromosome location?
FWIW, this seems to also be an issue in A3SS.hg19.gff3
:
(obot_virtualenv)[obotvinnik@tscc-login2 prettyplotlib]$ grep exon ~/genomes/miso_annotations/hg19/A3SS.hg19.gff3 | head
chr1 A3SS exon 15796 15947 . - . ID=chr1:6470:6628:-@chr1:5805|5810:5659:-.A.coreAndExt;Parent=chr1:6470:6628:-@chr1:5805|5810:5659:-.A;gid=chr1:6470:6628:-@chr1:5805|5810:5659:-
chr1 A3SS exon 16607 16765 . - . ID=chr1:6470:6628:-@chr1:5805|5810:5659:-.A.up;Parent=chr1:6470:6628:-@chr1:5805|5810:5659:-.A;gid=chr1:6470:6628:-@chr1:5805|5810:5659:-
chr1 A3SS exon 15796 15942 . - . ID=chr1:6470:6628:-@chr1:5805|5810:5659:-.B.core;Parent=chr1:6470:6628:-@chr1:5805|5810:5659:-.B;gid=chr1:6470:6628:-@chr1:5805|5810:5659:-
chr1 A3SS exon 16607 16765 . - . ID=chr1:6470:6628:-@chr1:5805|5810:5659:-.B.up;Parent=chr1:6470:6628:-@chr1:5805|5810:5659:-.B;gid=chr1:6470:6628:-@chr1:5805|5810:5659:-
chr1 A3SS exon 17233 17742 . - . ID=chr1:7778:7924:-@chr1:7231|7605:7096:-.A.coreAndExt;Parent=chr1:7778:7924:-@chr1:7231|7605:7096:-.A;gid=chr1:7778:7924:-@chr1:7231|7605:7096:-
chr1 A3SS exon 17915 18061 . - . ID=chr1:7778:7924:-@chr1:7231|7605:7096:-.A.up;Parent=chr1:7778:7924:-@chr1:7231|7605:7096:-.A;gid=chr1:7778:7924:-@chr1:7231|7605:7096:-
chr1 A3SS exon 17233 17368 . - . ID=chr1:7778:7924:-@chr1:7231|7605:7096:-.B.core;Parent=chr1:7778:7924:-@chr1:7231|7605:7096:-.B;gid=chr1:7778:7924:-@chr1:7231|7605:7096:-
chr1 A3SS exon 17915 18061 . - . ID=chr1:7778:7924:-@chr1:7231|7605:7096:-.B.up;Parent=chr1:7778:7924:-@chr1:7231|7605:7096:-.B;gid=chr1:7778:7924:-@chr1:7231|7605:7096:-
chr1 A3SS exon 18268 18379 . - . ID=chr1:8776:14754:-@chr1:8232|8242:8131:-.A.coreAndExt;Parent=chr1:8776:14754:-@chr1:8232|8242:8131:-.A;gid=chr1:8776:14754:-@chr1:8232|8242:8131:-
chr1 A3SS exon 18913 24891 . - . ID=chr1:8776:14754:-@chr1:8232|8242:8131:-.A.up;Parent=chr1:8776:14754:-@chr1:8232|8242:8131:-.A;gid=chr1:8776:14754:-@chr1:8232|8242:8131:-
A5SS.hg19.gff3
:
(obot_virtualenv)[obotvinnik@tscc-login2 prettyplotlib]$ grep exon ~/genomes/miso_annotations/hg19/A5SS.hg19.gff3 | head
chr1 A5SS exon 17233 17368 . - . ID=chr1:7605:7469|7389:-@chr1:7096:7231:-.A.dn;Parent=chr1:7605:7469|7389:-@chr1:7096:7231:-.A;gid=chr1:7605:7469|7389:-@chr1:7096:7231:-
chr1 A5SS exon 17526 17742 . - . ID=chr1:7605:7469|7389:-@chr1:7096:7231:-.A.coreAndExt;Parent=chr1:7605:7469|7389:-@chr1:7096:7231:-.A;gid=chr1:7605:7469|7389:-@chr1:7096:7231:-
chr1 A5SS exon 17233 17368 . - . ID=chr1:7605:7469|7389:-@chr1:7096:7231:-.B.dn;Parent=chr1:7605:7469|7389:-@chr1:7096:7231:-.B;gid=chr1:7605:7469|7389:-@chr1:7096:7231:-
chr1 A5SS exon 17606 17742 . - . ID=chr1:7605:7469|7389:-@chr1:7096:7231:-.B.core;Parent=chr1:7605:7469|7389:-@chr1:7096:7231:-.B;gid=chr1:7605:7469|7389:-@chr1:7096:7231:-
chr1 A5SS exon 16854 17055 . - . ID=chr1:7924:7778|7469:-@chr1:6717:6918:-.A.dn;Parent=chr1:7924:7778|7469:-@chr1:6717:6918:-.A;gid=chr1:7924:7778|7469:-@chr1:6717:6918:-
chr1 A5SS exon 17606 18061 . - . ID=chr1:7924:7778|7469:-@chr1:6717:6918:-.A.coreAndExt;Parent=chr1:7924:7778|7469:-@chr1:6717:6918:-.A;gid=chr1:7924:7778|7469:-@chr1:6717:6918:-
chr1 A5SS exon 16854 17055 . - . ID=chr1:7924:7778|7469:-@chr1:6717:6918:-.B.dn;Parent=chr1:7924:7778|7469:-@chr1:6717:6918:-.B;gid=chr1:7924:7778|7469:-@chr1:6717:6918:-
chr1 A5SS exon 17915 18061 . - . ID=chr1:7924:7778|7469:-@chr1:6717:6918:-.B.core;Parent=chr1:7924:7778|7469:-@chr1:6717:6918:-.B;gid=chr1:7924:7778|7469:-@chr1:6717:6918:-
chr1 A5SS exon 14363 16765 . - . ID=chr1:6918:6739|6721:-@chr1:4226:6628:-.A.dn;Parent=chr1:6918:6739|6721:-@chr1:4226:6628:-.A;gid=chr1:6918:6739|6721:-@chr1:4226:6628:-
chr1 A5SS exon 16858 17055 . - . ID=chr1:6918:6739|6721:-@chr1:4226:6628:-.A.coreAndExt;Parent=chr1:6918:6739|6721:-@chr1:4226:6628:-.A;gid=chr1:6918:6739|6721:-@chr1:4226:6628:-
MXE.hg19.gff3
:
(obot_virtualenv)[obotvinnik@tscc-login2 prettyplotlib]$ grep exon ~/genomes/miso_annotations/hg19/MXE.hg19.gff3 | head
chr1 MXE exon 764383 764484 . + . ID=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.A.up;Parent=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.A;gid=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+
chr1 MXE exon 776580 776753 . + . ID=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.A.mxe1;Parent=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.A;gid=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+
chr1 MXE exon 787307 788090 . + . ID=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.A.dn;Parent=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.A;gid=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+
chr1 MXE exon 764383 764484 . + . ID=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.B.up;Parent=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.B;gid=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+
chr1 MXE exon 783034 783186 . + . ID=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.B.mxe2;Parent=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.B;gid=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+
chr1 MXE exon 787307 788090 . + . ID=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.B.dn;Parent=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+.B;gid=chr1:754246:754347:+@chr1:766443:766616:+@chr1:772897:773049:+@chr1:777170:777953:+
chr1 MXE exon 1027371 1027483 . - . ID=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.B.dn;Parent=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.B;gid=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-
chr1 MXE exon 1041336 1041429 . - . ID=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.B.mxe2;Parent=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.B;gid=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-
chr1 MXE exon 1051440 1051736 . - . ID=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.B.up;Parent=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.B;gid=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-
chr1 MXE exon 1027371 1027483 . - . ID=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.A.dn;Parent=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-.A;gid=chr1:1041303:1041599:-@chr1:1040265:1040318:-@chr1:1031199:1031292:-@chr1:1017234:1017346:-
RI.hg19.gff3
:
(obot_virtualenv)[obotvinnik@tscc-login2 prettyplotlib]$ grep exon ~/genomes/miso_annotations/hg19/RI.hg19.gff3 | head
chr1 RI exon 17233 17742 . - . ID=chr1:7464:7605:-@chr1:7096:7227:-.A.withRI;Parent=chr1:7464:7605:-@chr1:7096:7227:-.A;gid=chr1:7464:7605:-@chr1:7096:7227:-
chr1 RI exon 17233 17364 . - . ID=chr1:7464:7605:-@chr1:7096:7227:-.B.dn;Parent=chr1:7464:7605:-@chr1:7096:7227:-.B;gid=chr1:7464:7605:-@chr1:7096:7227:-
chr1 RI exon 17601 17742 . - . ID=chr1:7464:7605:-@chr1:7096:7227:-.B.up;Parent=chr1:7464:7605:-@chr1:7096:7227:-.B;gid=chr1:7464:7605:-@chr1:7096:7227:-
chr1 RI exon 17233 17742 . - . ID=chr1:7469:7605:-@chr1:7096:7231:-.A.withRI;Parent=chr1:7469:7605:-@chr1:7096:7231:-.A;gid=chr1:7469:7605:-@chr1:7096:7231:-
chr1 RI exon 17233 17368 . - . ID=chr1:7469:7605:-@chr1:7096:7231:-.B.dn;Parent=chr1:7469:7605:-@chr1:7096:7231:-.B;gid=chr1:7469:7605:-@chr1:7096:7231:-
chr1 RI exon 17606 17742 . - . ID=chr1:7469:7605:-@chr1:7096:7231:-.B.up;Parent=chr1:7469:7605:-@chr1:7096:7231:-.B;gid=chr1:7469:7605:-@chr1:7096:7231:-
chr1 RI exon 17606 18061 . - . ID=chr1:7778:7924:-@chr1:7469:7605:-.A.withRI;Parent=chr1:7778:7924:-@chr1:7469:7605:-.A;gid=chr1:7778:7924:-@chr1:7469:7605:-
chr1 RI exon 17606 17742 . - . ID=chr1:7778:7924:-@chr1:7469:7605:-.B.dn;Parent=chr1:7778:7924:-@chr1:7469:7605:-.B;gid=chr1:7778:7924:-@chr1:7469:7605:-
chr1 RI exon 17915 18061 . - . ID=chr1:7778:7924:-@chr1:7469:7605:-.B.up;Parent=chr1:7778:7924:-@chr1:7469:7605:-.B;gid=chr1:7778:7924:-@chr1:7469:7605:-
chr1 RI exon 14407 16765 . - . ID=chr1:4833:6628:-@chr1:4270:4692:-.A.withRI;Parent=chr1:4833:6628:-@chr1:4270:4692:-.A;gid=chr1:4833:6628:-@chr1:4270:4692:-
And TandemUTR.hg19.gff3
:
(obot_virtualenv)[obotvinnik@tscc-login2 prettyplotlib]$ grep exon ~/genomes/miso_annotations/hg19/TandemUTR.hg19.gff3 | head
chr19 TandemUTR exon 10663759 10664625 . - . ID=chr19:10525223:10525625:-@chr19:10524759:10525222:-.A.coreAndExt;Parent=chr19:10525223:10525625:-@chr19:10524759:10525222:-.A;gid=chr19:10525223:10525625:-@chr19:10524759:10525222:-
chr19 TandemUTR exon 10664223 10664625 . - . ID=chr19:10525223:10525625:-@chr19:10524759:10525222:-.B.core;Parent=chr19:10525223:10525625:-@chr19:10524759:10525222:-.B;gid=chr19:10525223:10525625:-@chr19:10524759:10525222:-
chr1 TandemUTR exon 227918925 227920091 . - . ID=chr1:225986625:225986714:-@chr1:225985548:225986624:-.A.coreAndExt;Parent=chr1:225986625:225986714:-@chr1:225985548:225986624:-.A;gid=chr1:225986625:225986714:-@chr1:225985548:225986624:-
chr1 TandemUTR exon 227920002 227920091 . - . ID=chr1:225986625:225986714:-@chr1:225985548:225986624:-.B.core;Parent=chr1:225986625:225986714:-@chr1:225985548:225986624:-.B;gid=chr1:225986625:225986714:-@chr1:225985548:225986624:-
chr7 TandemUTR exon 89861938 89866931 . + . ID=chr7:89699874:89703121:+@chr7:89703122:89704867:+.A.coreAndExt;Parent=chr7:89699874:89703121:+@chr7:89703122:89704867:+.A;gid=chr7:89699874:89703121:+@chr7:89703122:89704867:+
chr7 TandemUTR exon 89861938 89865185 . + . ID=chr7:89699874:89703121:+@chr7:89703122:89704867:+.B.core;Parent=chr7:89699874:89703121:+@chr7:89703122:89704867:+.B;gid=chr7:89699874:89703121:+@chr7:89703122:89704867:+
chr3 TandemUTR exon 111710568 111712215 . + . ID=chr3:113193258:113193388:+@chr3:113193389:113194905:+.A.coreAndExt;Parent=chr3:113193258:113193388:+@chr3:113193389:113194905:+.A;gid=chr3:113193258:113193388:+@chr3:113193389:113194905:+
chr3 TandemUTR exon 111710568 111710698 . + . ID=chr3:113193258:113193388:+@chr3:113193389:113194905:+.B.core;Parent=chr3:113193258:113193388:+@chr3:113193389:113194905:+.B;gid=chr3:113193258:113193388:+@chr3:113193389:113194905:+
chr20 TandemUTR exon 6055491 6057818 . - . ID=chr20:6004667:6005818:-@chr20:6003491:6004666:-.A.coreAndExt;Parent=chr20:6004667:6005818:-@chr20:6003491:6004666:-.A;gid=chr20:6004667:6005818:-@chr20:6003491:6004666:-
chr20 TandemUTR exon 6056667 6057818 . - . ID=chr20:6004667:6005818:-@chr20:6003491:6004666:-.B.core;Parent=chr20:6004667:6005818:-@chr20:6003491:6004666:-.B;gid=chr20:6004667:6005818:-@chr20:6003491:6004666:-
I have run Miso (great manual), but it is not pulling out my gene (2 Exons knocked out)
What settings do I need to include transcripts with low to no reads compared to the control?
I'm trying filter_results = False min_event_reads = 0 at the moment.
Thanks alig
Check for presence of BAM index (.bai
) in the same directory as the BAM.
Within a single data set. This seems to be needed for working with Trinity output files.
I tried to run MISO to estimate insert size and compute-genes-psi
With identical parameters, annotation file provided by MISO and dataset.
Both insert size stimate and compute psi failed for BAM file generated from MapSplice and SpliceMap (both latest version). Only Tophat output's BAM run smoothly.
e.g. for SpliceMap and MapSplice's BAM, during compute-genes-psi, no files are output to output-directory. It always shows "only 0 reads in gene, skipping...."
Would like to ask which reads mapper were tested?
Thanks.
Read only the reads for a given gene.
Add proper handling of "five_prime_utr" and "three_prime_utr" to GFF parser
Allowed by GFF3 format.
I tried to run sashimi plot in 2 Ubuntu systems, both comes with Python 2.6.5.
When I execute sashimi plot by python python plot.py --plot-insert-len xxx.insert_len --output-dir plots/
it ways halts with "Error: need --output-dir"
I checked on the source code a bit.
if options.output_dir == None:
print "Error: need --output-dir"
sys.exit(1)
It seems like .output_dir is not correctly parsed by OptionParser.
I have installed matplotlib, pysam and scipy in both systems.
Fix up RPKM labels and give better vertical alignment of Psi tracks.
Right now only M and N tags are recognized, and behavior is undefined for others.
Script to check that the BAM headers (chromosome names) and the GFF headers match, i.e. that UCSC genome mapped reads are not being run on Ensembl derived events, or vice versa, to help users debug.
Use gffutils
to:
gene_id=
in attributes field of all children records of a gene
entrySE
-style events)Use annotated GFF files as a substitute for current annotations on website.
Make MISO output a list of job IDs when used on the cluster. Make a companion script that checks if all the jobs have finished.
"""
miso_zip.py does not work for Ensembl style chromosome titles. I think this is because sql tables cannot have integer names hence
CREATE TABLE 11 (...)
fails.
I added an incredibly naive patch that appends chr to the chromosome name if it doesn't already start with 'chr', though I'm sure something more extensible exists.
Cheers,
Isaac
"""
This happens if you only read a region, for paired-end reads, obviously. It seems that it is a samtools bug.
Implement --lazy
flag for running MAP estimate MISO in special case of single-end (no sampling, no BFs). Only outputs summary files.
GFF3 causes major issues. Switch to GTF format, while keeping GFF3 support (internally convert to GTF).
Creates excessive number of files currently. If there is user interest, willing to implement an sqlite database that stores the delta posteriors - this will dramatically reduce the number of files and the footprint, will be universally accessible, etc.
Switch to @daler 's gffutils from current hacky GFF parser. Find gene model abstraction that fits with minimal pain. Perform speed benchmarks between current parser and gffutils.
Re: request from UNC users.
Hello,
Using miso
on our cluster, I get:
$ miso
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
/home/yeo-lab/software/bin/miso: line 10: from: command not found
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
import: unable to open X server `' @ import.c/ImportImageCommand/359.
/home/yeo-lab/software/bin/miso: line 20: from: command not found
/home/yeo-lab/software/bin/miso: line 21: from: command not found
/home/yeo-lab/software/bin/miso: line 22: from: command not found
import: unable to open X server `' @ import.c/ImportImageCommand/359.
/home/yeo-lab/software/bin/miso: line 25: syntax error near unexpected token `('
/home/yeo-lab/software/bin/miso: line 25: `miso_path = os.path.dirname(os.path.abspath(__file__))'
I thought it might have been some incorrect compilation on our server-side, so I installed it in an environment where I have total control (my laptop), but I get the same error:
$ git clone [email protected]:yarden/MISO
$ cd MISO
$ python setup.py build ; sudo python setup.py install
$ sudo miso
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 5: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 6: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 7: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 8: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 9: import: command not found
from: can't read /var/mail/collections
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 12: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 14: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 15: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 16: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 17: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 18: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 19: import: command not found
from: can't read /var/mail/misopy.parse_csv
from: can't read /var/mail/misopy.settings
from: can't read /var/mail/misopy.settings
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 23: import: command not found
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 25: syntax error near unexpected token `('
/Library/Frameworks/EPD64.framework/Versions/Current/bin/miso: line 25: `miso_path = os.path.dirname(os.path.abspath(__file__))'
This is the exact same error as I get when I run just plain miso
, without sudo
. I tried sudo
because I thought the error with can't read /var/mail/misopy.parse_csv
might be because of permissions.
Please let me know how I may correctly install MISO.
Thank you,
Olga
Hi Yarden,
What about something like this: http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.aoas/1318514284 for a tack on module at the end to handle biological replicates for calling the event-level differential splicing? I think you might get more uptake of MISO if it handled replicates automatically.
Use kuler and/or equispacing (similar to ggplot2) to create default color schemes for sashimi plots. Make colors
argument in settings file optional.
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