jts / mbtools Goto Github PK

Hi guys,

I am trying to use mbtools but am getting zero total_calls and modified_calls for all reads. My data is modbams called with dorado using model [email protected] and --modified-bases 5mCG_5hmCG.

Any idea how to address this problem? Has anybody experienced this issue?

Many thanks!
Rodrigo

It seems bam2pat for nanopore data has some problem in recognising "eXtended CIGAR", or CIGARX string.

8,229,233,213,224,53,229,57,235,252,255,255,115,249,247,185,231,247,57,139,181,235,251,74,126,165,34,254,255,170,186,193,255,255,254,241,235,237,255,255,254,238,225,14,254,238,253,255,66,254,254,247  RG:Z:c969ee83   mc:f:99.5874    mg:f:99.6108    NM:i:72     
[ patter ] [ patter ] Unknown CIGAR character: =                                                                                                                                                      
[ patter ] [ chr9 ] Exception while processing line 798. Line content:                                                                                                                                                                                              
m64101_220704_113609/114427486/ccs      0       chr9    239949  60      8034=1I565=4D2297=      *       0       10900   ATTTCCAGTTATTCACATTAGAAACAGTACACCACTGAATAAATTTATGCATTCATCTTTGCTTACCTCTTTAATGATTCTTCACGATAAATGCTAGAAATAGAACCACAGACTTAAAGGTCTCCATTGATATGTGTGGC

Hello all, thanks for the great tool it helped us solve a conversion that modbam2bed failed to handle.

That being said I have run into a little issue. When i try to set the probability-threshold option with reference-frequency i can't seem to get it take effect and it stays at 0.8. I have tried with a file to make sure that the number of called bases remains the same regardless of what i set -t as.

Thanks again for the great tool.

-Francesco

Hi Jared and Thanks for this tools.

I am trying to clone and run it but it seems like I am missing something or that something is missing in the repo.

There is no make or bash file and simply running " mbtools reference-frequency input.bam > output.tsv"
as in the README will not do. the rm file is not excusable.

Any suggestions?

Assaf

Hi, can you please let me know how to install mbtools? I tried pip install mbtools but still cannot execute it. Thanks