how to get fasta files for list of genes?
I have list of genes like
LOC109802912
LOC109788332
LOC109789928
LOC109809764 ...
and have a fasta file like
>rna-XR_003803819.1 gene=LOC114915746
TGCTTCTTCTCTGTTGGAAGAGTTTAAAAGCAATAAAACTAAGTGTTTTGAGCTCTCTGAAATTGCTGGT
CATGTTGTTGAGTTCAGTGCGGATCAATATGGGAGCCGATTTATTCAGCAAAAGCTTGAAACAGCTActa
ca
>rna-XR_002239520.2 gene=LOC109794983
TCCTATTCATCATGCAGGATGTCAGAATCTTCATTTCAAATTGGACCAATCCTTCTTGTGAATGAACCCT
TCACGATTGATAATGGTCTAATGACACCTACTTTGAAAATTCGAAGAGATAGAGTTGTGGCTCAATACAG
G
how can i get the fasta sequences for genes?
1 answer
Try this:
pip install --user pyfaidx
xargs faidx -d " " YOURFASTA.fasta < GENEID_LIST.txt > extracted_sequences.fasta
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alexandru.bologa.marian •
I am using window
Please mention this from the beginning in your next questions. By using windows you are making things harder for yourself (because fewer tools are available) and for us (because most of us don't use windows for bioinformatics).
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WouterDeCoster
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Past threads with solutions for this:
Extract fasta sequences from a file using a list in another file.
How do I extract Fasta Sequences based on a list of IDs?