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I have downloaded from sourceforge.net the latest version of Bowtie2
bowtie2-2.2.3-source.zip and built bowtie2-build-s ok.
However when I run it on some of the examples at GCAT it gives
much worse results than the results given for Bowtie2 on the GCAT site.
View Full GCAT Alignment Report: 150 bowtie2 2_2_3 test5 JHU (150bp-pe-small-indel)
For example on the 150bp paired-end small indel benchmark I get 93.53%
Total Correct whereas (with an earlier version Bowtie2 2.1.0?) GAT got 97.02%
The SAM output file from Bowtie2 appears to be complete.
The bowtie2 command line I am using appears to be equivelent to that
used by GCAT.
Has anyone seen local versions of Bowtie2 behaving like this before?
Any ideas what I have done wrong?
Or errors to check for?
Many thanks
Bill
bowtie2-2.2.3-source.zip and built bowtie2-build-s ok.
However when I run it on some of the examples at GCAT it gives
much worse results than the results given for Bowtie2 on the GCAT site.
View Full GCAT Alignment Report: 150 bowtie2 2_2_3 test5 JHU (150bp-pe-small-indel)
For example on the 150bp paired-end small indel benchmark I get 93.53%
Total Correct whereas (with an earlier version Bowtie2 2.1.0?) GAT got 97.02%
The SAM output file from Bowtie2 appears to be complete.
The bowtie2 command line I am using appears to be equivelent to that
used by GCAT.
Has anyone seen local versions of Bowtie2 behaving like this before?
Any ideas what I have done wrong?
Or errors to check for?
Many thanks
Bill