How to extract gene IDs from a tabular file based on a list of locus tags?
I have a file like:
GeneID Locus tag Protein name
839580 AT1G01010 NAC domain containing protein 1
839569 AT1G01020 ARV1 family protein
839569 AT1G01020 ARV1 family protein
839569 AT1G01020 ARV1 family protein
I also have a list of locus tags (arround 5000) which I want to extract from the entire file.
e.g if I want to extract gene Id and protein name of
AT1G01010
AT1G01020
I should get
839580 NAC domain containing protein 1
839569 ARV1 family protein
• 2,421 views
•
link
updated
by
Alex Reynolds
•
written
by
majeedaasim •
•
written
by
majeedaasim •
2 answers
One approach using Unix tools:
$ grep -Fwf locusTags.txt geneAnnotations.txt > answer.txt
• 1 views
•
link
written
by
Alex Reynolds
Log in to answer this question.
More posts like this
-
replace the NP* accession in header of the fasta file with gene name using GFF file
written by najibveto •
-
Python Script that outputs axons from gff file to a new file
written by Michal Nevo •
-
How to extract fasta subsequences from a multiline fasta file which has very long headers ?
written by sunnykevin97
-
How to extract Locus tag from GeneIDs in NCBI for soybean database.
written by b.g.tamang •
-
Extract gene Name, ID, and description from gff3 file
written by akibio •
-
How to get intron sequence from GFF format?
written by vani2lasky99 •
-
Using HTseq-count for Pseudomonas Aeruginosa data
written by jspainhour3 •
-
Editing header by adding pipe in fasta file
written by muhammad.arslan •
-
Gene length from a GFF file to count RPKM for edgeR-RNA-seq analysis
written by pixie@bioinfo
-
compare 2 sequence using blast from different identification files
written by kws15 •
