Question: Way to trim all NGS nucleotide sequences to a specific section
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gravatar for c.l.frankling
14 days ago by
c.l.frankling10 wrote:

Is there a way to trim the nucleotide sequence to a specific region? I know you can by base number but what if say for instance I would like to trim to just the open reading frame e.g.

TATAGAAGGGTAATACGACTCACTATAGGGAGTCGCTGCCATGGCCTTGAAAGCCCATCTCGTAACGCCATCATTGGGAGGAGGA

and I want to trim everything before the ATG off so that it becomes;

ATGGCCTTGAAAGCCCATCTCGTAACGCCATCATTGGGAGGAGGA

This will be a different base position in most of the sequences so I couldn't instance trim off position 1-40. Is there a tool where you can tell it trim all sequences to the region starting with ATGGCC??

Many thanks,

Charlotte Frankling.

ADD COMMENTlink modified 13 days ago by Jennifer Hillman Jackson23k • written 14 days ago by c.l.frankling10
0
gravatar for Jennifer Hillman Jackson
13 days ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The regular trimming tools won't do this exact operation, but the tool Text Manipulation > Replace Text in entire line could be used. This would be appropriate for fasta formatted data where the sequence lines are not wrapped (use FASTA Width formatter as needed), but not fastq.

Hope that helps! Jen, Galaxy team

ADD COMMENTlink written 13 days ago by Jennifer Hillman Jackson23k
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