Question: How can I do trimming off to all nucleotide sequences that end with a specific sequence in my illumine reads?!
0
gravatar for dina.hany
19 months ago by
dina.hany0
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
0
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Dina,

The fastq QA/trimming tools available at http://usegalaxy.org 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.

Help: https://galaxyproject.org/tutorials/ngs/#fastq-manipulation-and-quality-control

Thanks! Jen, Galaxy team

ADD COMMENTlink written 19 months ago by Jennifer Hillman Jackson25k
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