Closed roryk closed 11 years ago
Rory; Thanks for these, great stuff. A couple of quick thoughts:
Rory; Sorry, missed the bowtie2 updates here. For the -X issue, it looks like bowtie2 also has this option: are you finding it doesn't work correctly? If so, I can merge away with your fixes.
Hi Brad,
Don't merge yet. Bowtie2 is working correctly. The behavior is changed in Bowtie2 so reads failing -X do not get filtered out, they get an optional discordant (YT:Z:DP) or unpaired (YT:Z:UP, if they are on different chromosomes) flag set. So filtering the list on that before calculating the insert sizes should fix the problem. I haven't got around to implementing that yet.
I'll close this pull request and open a clean one since most of the changes to it have been reverted.
Rory
On Jan 30, 2013, at 5:30 AM, Brad Chapman wrote:
Rory; Sorry, missed the bowtie2 updates here. For the -X issue, it looks like bowtie2 also has this option: are you finding it doesn't work correctly? If so, I can merge away with your fixes.
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1) Look for bowtie path as "bowtie" not "bowtie2" in program: when using bowtie2. 2) Fixed a dictionary getting mutated problem when adding options. 3) Bowtie2 does not seem to respect the -X parameter:
For the time being I changed the inner distance calculation around to use the median and remove any fragments > 3x the standard deviation but now that I write this, I realize I should just manually do -X when making the calculation.