Question: Clipping adapter from 3' end of only 1 of 2 paired end reads
gravatar for amy.klegarth
3.6 years ago by
U. Notre Dame
amy.klegarth0 wrote:

Hi all,

I cropped barcodes a long while back in a lab where I had CLC Genomics - now that I'm in a different lab I'd like to do some reprocessing of my files and when the barcodes were originally cropped I failed to remove a partial adapter of CGG from the 3' end of all my >filename/2 reads but not my  >filename/1 reads.  

Is there a way to use the clip or trim features to only take off the first three basepairs of the combined reads file, or do I need to split the fastq and then trim?


adapter 3' clip paired end • 991 views
ADD COMMENTlink modified 3.6 years ago by Jennifer Hillman Jackson25k • written 3.6 years ago by amy.klegarth0
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The two ends of the paired sequences should be in distinct files. Then run the Trim tool on the data that needs the extra clipping. If for some reason the sequences have been joined, back up to the step before they were joined, do the QC, then continue. 

Best, Jen, Galaxy team

ADD COMMENTlink written 3.6 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 167 users visited in the last hour