Bioscope is giving 180 million mapped reads and bowtie+tophat is 38 million. The data is strand specific SOLID data (~50 bp). Does any one about this mapping differences ?
Do a large number of your bioscope aligned reads have significant clipping?
does bioscope report unique alignments? did you set same mismatch threshold?
@GWW- How do you know whther reada are clipped are not (by looking at the length)?, I didn't quiet unsderstand the purpose of the question.
@Leszek - If I filter non-redundant/duplicate (the reads that have same chr-start and chr-end) reads, 180 mil becomes 38 million in Bioscope case. In Tophat, 38 million becomes 6 million. Should I use unique reads for my downstream analysis ?
For SOLID RNA-Seq Tophat seems to be doing worse than plain bowtie, at least in some cases.
Solid Split Rna-Seq Mapping