Question: (Closed) I have a fasta file with 2000 sequences (big.fasta) and a text file with 70 sequence ids (ids.txt). How can I remove (or cut and paste) the sequences in ids.txt from the big.fasta file?
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gravatar for hasche89
2.2 years ago by
hasche890
hasche890 wrote:

I have a fasta file with 2000 sequences (big.fasta) with transcripts.

I also have a text file with 70 sequence ids (ids.txt) present between those 2000 sequences.

I want to remove the sequences in ids.txt from the big.fasta file; thus creating a fasta file with 1930 sequences free of the ids from ids.txt.

Also, if possible can I cut and paste those 70 sequences from the 2000 sequences file to some other fasta file?

I am a novice with no prior experience in these matters. Kindly help.

bash rna-seq samtools bioperl perl • 779 views
ADD COMMENTlink modified 2.2 years ago by thackl2.4k • written 2.2 years ago by hasche890

Hello hasche89!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

PS: duplicate
ADD REPLYlink written 2.2 years ago by Pierre Lindenbaum101k
0
gravatar for thackl
2.2 years ago by
thackl2.4k
European Union
thackl2.4k wrote:

This would work:

git clone https://github.com/BioInf-Wuerzburg/SeqFilter.git
cd SeqFilter
make  # just fetches some libraries, no root or anything required

bin/SeqFilter big.fasta --ids idx.txt --ids-exclude --out big-filtered.fasta

 

ADD COMMENTlink written 2.2 years ago by thackl2.4k
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