3.7 years ago by
I have a doubt, I am working on strand specific protocol (fr-firststrand). When aligning the reads using bowtie2, do I need to explicitly mention as fr-firststrand.
If I am not mentioning in my bowtie2 command, will it affect my alignment result?
From Bowtie2 manual:
--fr/--rf/--ff - The upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand. E.g., if
--fr is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (
-X) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid.
--rf likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented.
--ff requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented. Default:
--fr (appropriate for Illumina's Paired-end Sequencing Assay).