humberto-ortiz / dmel-ercc Goto Github PK

2014/04/02 - HOZ

There are publically available datasets with dmel spike in data

Jiang L, Schlesinger F, Davis CA, Zhang Y et al. Synthetic spike-in
standards for RNA-seq experiments. Genome Res 2011
Sep;21(9):1543-51. PMID: 21816910

RNA-Seq on libraries made from External RNA Controls Consortium (ERCC)
external RNA controls, and a mixture of mRNA from Drosophila
melanogaster S2 cell and ERCC mRNAs.

We evaluated performance of RNA-Seq on known synthetic PolyA+ mRNAs
from the External RNA Controls Consortium (ERCC) alone and in mixtures
with PolyA+ mRNA from Drosophila S2 cells. ERCC mRNAs were obtained
under Phase V testing from the National Institutes of Standards and
Technology (NIST). The ERCC pool contained 96 species of mRNA of
various lengths and GC content covering a 2^20 concentration
range. Libraries were constructed using 100ng S2 mRNA with 5ng, 2.5ng,
or 1ng ERCC mRNAs, and using 50ng ERCC mRNA without S2 cell mRNA. Our
data shows an outstanding linear fit between RNA-Seq read density and
known input amounts.

GSM516588, GSM516589, GSM517059, GSM517060, GSM517061, GSM517062, and
GSE26284.

GSE20579 is

GSM517059       100ng_S2_5ng_ERCC_phaseV_pool15_mRNA-seq
GSM517060       100ng_S2_2.5ng_ERCC_phaseV_pool15_mRNA-seq
GSM517061       100ng_S2_1ng_ERCC_phaseV_pool15_mRNA
GSM517062       50ng_ERCC_phaseV_pool15_mRNA-seq

http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE20579&format=file

GSE20555 has dilutions of different runs:

GSM516588       100ng_library_methA_S2_2.5%ERCC_phaseV_pool15mRNA
GSM516589       100ng_library_methB_S2_2.5%ERCC_phaseV_pool15_mRNA
GSM516590       50ng_library_methB_S2_2.5%ERCC_phaseV_pool15_mRNA
GSM516591       10ng_library_methB_S2_2.5%ERCC_phaseV_pool15_mRNA
GSM516592       1ng_library_methB_S2_2.5%ERCC_phaseV_pool15_mRNA
GSM516593       0.4ng_library_methB_S2_2.5%ERCC_phaseV_pool15_mRNA
GSM516594       0.01ng_library_methB_S2_2.5%ERCC_phaseV_pool15_mRNA

Supplemental table S2 shows % reads mapped to genomes and measured
concentrations.

2014/04/07 - HOZ

See http://useq.sourceforge.net/cmdLnMenus.html#RNASeqSimulator and
http://cbil.upenn.edu/BEERS/

for other simulators

2014/05/01 - HOZ

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20579

  612  wget -c http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE20579&format=file
  614  cat index.html\?acc\=GSE20579 |grep tar
  615  wget -c "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE20nnn/GSE20579/suppl/GSE20579_RAW.tar"

SAM files? no, bowtie tab files. 

apt-get install python-virtualenv

  647  sudo apt-get install virtualenvwrapper
  654  source /etc/bash_completion.d/virtualenvwrapper
  655  mkvirtualenv dmel
  657  pip install pysam

http://pysam.readthedocs.org/en/latest/

samtest.py

install samtools

/usr/share/samtools/bowtie2sam.pl GSM517059_run29_s_1_ERCC_dm3_map.txt > test.sam

2014/10/25 - HOZ

workon dmel to load virtual environment
lsvirtualenv to list them

test.sam is missing headers, can't load into pysam:

https://code.google.com/p/pysam/issues/detail?id=73

See the cogent package, it can parse bowtie files.

cogent-test.py

2014/11/01 - HOZ

cogent is part of QIIME. MacQiime is installed on the Mac, and hulk
has /usr/local/qiime/activate.sh

2014/11/02 - HOZ

Pass mapfile as a positional argument, using argparse module.