View Single Post
Old 04-01-2014, 09:34 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

Can you post a reproducible example? The simplest way to do this would be to:

Code:
samtools sort -@ 4 namesorted_sample.bam sorted_sample
samtools index sorted_sample.bam
samtools view sorted_sample.bam 19:53864080-53867080 > subset.sam
and then post "subset.sam" somewhere (an attachment here, copy.com, dropbox, where ever). That should correspond to exonic_bin number 19 (at least it does on GRCm38.71). Then we can look at exactly why things are wonky.
dpryan is offline   Reply With Quote