Hi,
As I am about to use MMSeq and MMDiff for differential expression analysis in RNA-Seq, I have been looking at the github repository. I have been reading all MMSeq advices and understand their choices.
However, I do not understand: why should Bowtie1 be used and not Bowtie2 ? In fact, when I use Bowtie1, I have 49% of mapped reads (35% with default parameters) ; by contrast, I have a 97% of mapped reads with Bowtie2 (corresponding parameters have the same value) and 95% with default parameters. Please, note that each alignment have been performed against transcripts (fasta format) and that reads are under fasta format (no fastq quality scores).
Up to now, I have not tried to run MMSeq from Bowtie2, as I do not understand why it should not be done.
Would you mind helping me ? Thanks in advance !