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

Join Date: Jul 2011
Posts: 3,480

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

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,, 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.
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