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Question: Extract chromosome sequences from genome fasta file
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gravatar for h.stotz
2.5 years ago by
h.stotz • 20
European Union
h.stotz • 20 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 • 1.5k views
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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by h.stotz • 20
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gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k
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