Question: How can I do trimming off to all nucleotide sequences that end with a specific sequence in my illumine reads?!
gravatar for dina.hany
19 months ago by
dina.hany0 wrote:

Hello everyone,

I am new to Galaxy and I was wondering if anybody knows how can I trim all sequences that ends with a certain base sequences in my illumina reads?! for example, if i have this read: NTGTGGAAAGGACGAAACACCGTAATGGGTGGCGTTACTGGCGTTTTAGA and I want to trim off the bolded sequences from left till the CACCG sequence.

I will appreciate any help.

Thank you in advance.

Dina Hany

trimming fastq • 589 views
ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson25k • written 19 months ago by dina.hany0
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Dina,

The fastq QA/trimming tools available at are:

NGS: QC and manipulation

  • Trimmomatic flexible read trimming tool for Illumina NGS data
  • Trim Galore! adaptive quality and adapter trimmer
  • Trim sequences
  • FASTQ Trimmer by column
  • FASTQ Quality Trimmer by sliding window

Each will trim with slightly different results. Please review the tools forms, try a few out, and determine the one that is the best fit for your data. The tool FastQC can be used to evaluate the results before and after QA/trimming.


Thanks! Jen, Galaxy team

ADD COMMENTlink written 19 months 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: 173 users visited in the last hour