Question: Bioscope Vs Bowtie+Tophat
1
gravatar for Curiosity
9.0 years ago by
Curiosity120
Curiosity120 wrote:

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 ?

rna • 1.8k views
ADD COMMENTlink written 9.0 years ago by Curiosity120

Do a large number of your bioscope aligned reads have significant clipping?

ADD REPLYlink written 9.0 years ago by Gww2.7k

does bioscope report unique alignments? did you set same mismatch threshold?

ADD REPLYlink written 9.0 years ago by Leszek4.1k

@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 ?

ADD REPLYlink written 9.0 years ago by Curiosity120
0
gravatar for Darked89
9.0 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:

For SOLID RNA-Seq Tophat seems to be doing worse than plain bowtie, at least in some cases.

Solid Split Rna-Seq Mapping

ADD COMMENTlink modified 13 months ago by RamRS30k • written 9.0 years ago by Darked894.2k
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