User:Lindenb/Notebook/UMR915/20110202: Difference between revisions
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(New page: {{PLNB|20110201|20110203}} =Proteomics= Added some features for Céline's program =Project 'B'= wrote a tool to test whether a BAM file is sorted: https://gist.github.com/807481 . Asked fo...) |
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{{PLNB|20110201|20110203}} | {{PLNB|20110201|20110203}} | ||
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=Proteomics= | =Proteomics= | ||
Added some features for Céline's program | Added some features for Céline's program | ||
=Project 'B'= | =Project 'B'= | ||
wrote a tool to test whether a BAM file is sorted: https://gist.github.com/807481 . Asked for help on the samtools mailing list to improve the code. | * end of markdup, now indexing and running the GATK for CountCovariates. I wanted to use --DBSNP=(...)/dbsnp_130_b36.rod but there is no "chr" prefix for the chromosome. So I created <pre>sed 's/\t/\tchr/' dbsnp_130_b36.rod > dbsnp_130_hg18.rod</pre> | ||
wrote a tool to test whether a BAM file is sorted: https://gist.github.com/807481 . [http://sourceforge.net/mailarchive/message.php?msg_id=26996499 Asked for help on the samtools mailing list] to improve the code. | |||
<html><script src="https://gist.github.com/807481.js?file=bamsorted.c"></script></html> | <html><script src="https://gist.github.com/807481.js?file=bamsorted.c"></script></html> | ||
Latest revision as of 07:42, 2 February 2011
Proteomics
Added some features for Céline's program
Project 'B'
- end of markdup, now indexing and running the GATK for CountCovariates. I wanted to use --DBSNP=(...)/dbsnp_130_b36.rod but there is no "chr" prefix for the chromosome. So I created
sed 's/\t/\tchr/' dbsnp_130_b36.rod > dbsnp_130_hg18.rod
wrote a tool to test whether a BAM file is sorted: https://gist.github.com/807481 . Asked for help on the samtools mailing list to improve the code. <html><script src="https://gist.github.com/807481.js?file=bamsorted.c"></script></html>
