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Forum: RNA Sequencing 01-09-2015, 06:42 AM
Replies: 1
Views: 871
Posted By bbm
I also understand Tophat is splice-aware. My data...

I also understand Tophat is splice-aware. My data is transcriptome (mRNA), I expect Tophat to map at a similar rate to Bowtie. One difference is tophat maps reads that span splice junctions, right?
Forum: RNA Sequencing 01-09-2015, 06:30 AM
Replies: 1
Views: 871
Posted By bbm
Different Results Of Tophat2 And Bowtie2

Hello all,

I ran the same fastq file with tophat2 and bowtie2, and got very different mapping rates. I wonder if any of you will help me on this puzzle. It is single-end, 60-100 bp after trimming....
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