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Question: Remove duplicate sequences with same id from a fasta file
1
gravatar for CB
3.2 years ago by
CB • 10
US
CB • 10 wrote:

Dear all, there are many posts about remove duplicate sequences in a fasta file (https://www.biostars.org/p/3003/), but I want to remove only the duplicate sequences with the same ids.

I have many duplicate sequences in my fasta file, but with different ids and I want to keep them.

How to remove only same id sequence duplicates? I have protein sequences and my sequences are split in different lines.
duplicate sequence remove fasta • 3.9k views
ADD COMMENT • link •
modified 3.2 years ago by Alex Reynolds ♦ 29k • written 3.2 years ago by CB • 10

BBMap's Dedupe utility has a "requirematchingnames" flag. This will make it only remove duplicates that have identical sequence and identical names. For example:

dedupe.sh in=file.fasta out=deduped.fasta ac=f requirematchingnames

One copy of each duplicate set will remain, unless you add the "uniqueonly" flag.

ADD REPLY • link modified 3.2 years ago • written 3.2 years ago by Brian Bushnell ♦ 17k
3
gravatar for shenwei356
3.2 years ago by
shenwei356 ♦ 5.1k
China
shenwei356 ♦ 5.1k wrote:

http://bioinf.shenwei.me/seqkit/usage/#rmdup
ADD COMMENT • link written 3.2 years ago by shenwei356 ♦ 5.1k

It worked very well. It is very easy to use. Thanks!

ADD REPLY • link written 3.2 years ago by CB • 10
2
gravatar for Alex Reynolds
3.2 years ago by
Alex Reynolds ♦ 29k
Seattle, WA USA
Alex Reynolds ♦ 29k wrote:

Make your FASTA files single-line (one line for header, one line for sequence): Multiline Fasta To Single Line Fasta

Then:

$ awk '{ if (($0 ~ /^>/) && (!seen[$0]++)) { print $0; printSeq=1; } else if (($0 ~ /^[^>]/) && printSeq) { print $0; printSeq=0; }  }' in.fa > out.fa
ADD COMMENT • link modified 3.2 years ago • written 3.2 years ago by Alex Reynolds ♦ 29k
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