Hi,
I have short reads (max 50 nts, mostly 20-40 nts) that are from a stranded ligated Illumina library. I could't find if Bowtie2 has a stranded option so I use the TopHat fr-secondstrand option. But I don't expect my reads to be spliced so is there an option to skip the read segmentation? Or should I use other mappers for this job?
Thanks,
Jon
I have short reads (max 50 nts, mostly 20-40 nts) that are from a stranded ligated Illumina library. I could't find if Bowtie2 has a stranded option so I use the TopHat fr-secondstrand option. But I don't expect my reads to be spliced so is there an option to skip the read segmentation? Or should I use other mappers for this job?
Thanks,
Jon
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