Question: Extract chromosome sequences from genome fasta file
0
gravatar for h.stotz
24 months ago by
h.stotz10
European Union
h.stotz10 wrote:

I loaded genome sequences into Galaxy as fasta files. The files contain sequence information about chromosome, e.g.

chrA01 ATCGGATC etc. until the end of the chromosme sequence The next chromsome starts as chrA02 GGCCATA etc.

Can I grep the individual chromosomes?

galaxy • 1.1k views
ADD COMMENTlink modified 24 months ago by Jennifer Hillman Jackson25k • written 24 months ago by h.stotz10
0
gravatar for Jennifer Hillman Jackson
24 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The Filter tool can be used to extract individual chromosomes. The example on the tool form covers this exact case.

Convert fasta to tabular and use Filter. After, convert back to fasta and wrap the lines.

Best, Jen, Galaxy team

ADD COMMENTlink written 24 months ago by Jennifer Hillman Jackson25k
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