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Old 02-05-2014, 12:55 AM   #1
Location: Urbana Illinois

Join Date: Jan 2013
Posts: 28
Default Align paired and unpaired reads with Tophat

I have a stranded PE RNAseq data set that I want to align with tophat using the --library-type fr-firststrand option. After adaptor trimming I end up with my 4 files:


Is there a way to align these so I do not loose the strand information for the unpaired reads? When I run tophat with the files listed like this:

paired_1,unpaired_1 paired_2,unpaired_2

It seems to want to try and align the two unpaired files as paired files. If I combine the two unpaired files and run tophat with the files listed like this:

paired_1 paired_2,unpaired

It recognizes the last file as unpaired. But am I loosing my strand specificity by aligning this way? Thanks.
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