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:
paired_1
paired_2
unpaired_1
unpaired_2
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.
paired_1
paired_2
unpaired_1
unpaired_2
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.
Comment