Identifying Gene name

Question

[sicat.paolo20]

I am currently having a problem with Identifying gene names. I have the gtf, gff, and sam files. I can identify the gene because I have information about their position and I could just search seqeunce however my list is over a thousand. Is there any way I can do this without doing it one by one manually?

[Pierre Lindenbaum]

it's not clear, from which file do you need to get the gene name ? why do you cite the BAM ? why do you search the "sequence" ?

[sicat.paolo20]

at some point I lost my gene names and got tagged by something else. sequences still matched though.

[Pierre Lindenbaum]

it's kamoulox

[GenoMax]

Your GTF/GFF files should have the sequence names (if they are properly formatted). They are text files and you should be able to less|more filename to view contents. Post a few lines here by doing head -5 gtf/gff_file

[sicat.paolo20]

at some point I lost my gene names and got tagged by something else. sequences still matched though.

[GenoMax]

Not exactly sure what you are referring to. You should never have to modify gff/gtf files when you do any analysis.

[cpad0112]

use grep in linux/OS X.

$ grep "genesymbol" <input gtf,gff>

if you have gene symbols in a file

$ grep -f "gene_symbols_file" <input gtf/gff>