Question: Tophat2 Bowtie2 inchoerent results?
0
gravatar for Bio_ysl
5.5 years ago by
Bio_ysl20
Spain
Bio_ysl20 wrote:

I am trying to align paired-end data from Illumina (300bp x 2) to a draft genome. First of all I use Trimmomatic to remove adapters and bad quality ends. later I tried to map the reads; first with Bowtie2 alone and later with TopHat2 (which uses Bowtie2).

Bowtie2 alone mapped about 68% of the reads while Tophat about 40%, with which parameters is TopHat calling Bowtie that the alignment rate decrease instead of increasing?  Since the reads are quite long (up to 300nuc) should I modify the "--read-edit-dist" and "-N" parameters  (in this way I get more percentage of mapped reads, but I don't know if I'm getting ad alignments)?

Thank you very much

 

mapping rna-seq ngs tophat bowtie2 • 1.6k views
ADD COMMENTlink written 5.5 years ago by Bio_ysl20

AFAIK, tophat2 uses more strict default settings. For example tophat2 allows only 3 mismatches with default settings. There is a lot more stuff different but I can't tell from the top of my head. Therefore just try some different settings!

 

Best

ADD REPLYlink written 5.4 years ago by Phil S.660
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1862 users visited in the last hour