Question: Tophat Paired End Read
0
gravatar for 杨继文
6.6 years ago by
杨继文210
杨继文210 wrote:
Hi all, I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate files. Before mapping, I need to trim the reads. My questions is : Do I have to join pair end reads before timming, and then split again for Tophat??? Lookiong forward to your answers. Thanks Jiwen
rna-seq tophat • 1.8k views
ADD COMMENTlink modified 6.6 years ago by Jennifer Hillman Jackson25k • written 6.6 years ago by 杨继文210
0
gravatar for Jennifer Hillman Jackson
6.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Jiwen, No, you do not need to join the files for the quality processing. Hopefully this helps! Best, Jen Galaxy team
ADD COMMENTlink written 6.6 years ago by Jennifer Hillman Jackson25k
Jiwen, I wonder if you are thinking about the situation where you could be discarding reads that are to short after trimming?. In that case you could be getting the two files out of sync. If this is the case, I think you do need to join the files first, do the trimming and then take them apart again. Regards, Carlos
ADD REPLYlink written 6.6 years ago by Carlos Borroto390
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 16.09
Traffic: 173 users visited in the last hour