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Old 05-24-2016, 03:02 AM   #1
meabh
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Location: Ireland

Join Date: Aug 2015
Posts: 1
Default Is there a difference between a .sam produced by tophat2 and bowtie2?

I hope this makes sense,

So I have a perl script that is written to take the accepted_hits.bam file from tophat2, in sam format as an input. Unlike the original paper, I need the unmapped reads as a fastq file so I'm using bowtie2 to map, as it has this option also it outputs mapped results as a sam file so I don't need to convert it. My question is do these files have the same columns or not? It would seem fruitless to try this if tophat2 and bowtie2 output different columns etc.



Thanks

Edit. I don't know how I missed in the tophat manual that you can use the --no-convert-bam to output the result as sam, which means I don't need to use bowtie2 instead

Last edited by meabh; 05-24-2016 at 06:51 AM. Reason: I didn't realise you could output sam file from tophat2 which makes the question redundant
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