July 2010
1 post
4 tags
From Tophat to Pysam
I recently needed to interact with a SAM file in python that was created as part of a Tophat run. Rather rolling my own parser I decided to use the handy pysam module. However, I immediately ran into trouble. I couldn’t get pysam to open my file. It turns out pysam requires a BAM file not a SAM file. This meant I need to convert filetypes. So, I fired up samtools and tried a conversion.
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