Renaming fasta files with chromosomes
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2.5 years ago
namea38 • 0

I have a .fasta file that I'm trying to use bedtools getfasta on. When I run it I get the error

which I think is because my .fasta headers look like this

>HWI-D00270:252:CB1D5ANXX:8:1303:19141:48584/1
ACAGCTGATTAGACACAATGTCAACAAAGTACTGAAGACCAGAGAAAAACACTTATTATACTC
TTTGTTTTCAGGTGTGGAATGTGCTTTCTACCACGGCTACAAATACTACAAAGGATGTAGTA


and not like this

>chrI
ACAGCTGATTAGACACAATGTCAACAAAGTACTGAAGACCAGAGAAAAACACTTATTATACTC
TTTGTTTTCAGGTGTGGAATGTGCTTTCTACCACGGCTACAAATACTACAAAGGATGTAGTA


Is there a way I can edit the header to reflect only the chromosome.

fasta chromosome bedtools • 1.3k views
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You appear to have Illumina reads converted into fasta format in first example. That does not appear to be chromosome data at all.

Are you using a bed file for the intervals? What does it look like?

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I have a bed file I downloaded from the USCS genome browser

chrI 2653 2738 (TAG)n 322 +

chrI 2974 3011 AT_rich 30 +

chrI 3034 3069 AT_rich 21 +

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Why are you using a file with Illumina read data in fasta format instead of using the genome sequence file from UCSC? I assume you want to retrieve the fasta sequence corresponding to those intervals?

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Yeah I'm trying to use the DNA my lab sequenced from a particular region to look for transposons