How to subset a bed or gtf file to some genes of interest?

Question

[cyril-cros]

Hi,

I have a list of genes of particular interest to me, and some data I obtained from RNASeq / official annotation in GTF format (I can easily convert to the bed format with gtf2bed). They contain an identifier for each gene or transcript.
I would like to do some operations (compare my data to the official annotation for example), but ONLY on these genes of interest. I select them as having the same gene ontology for example.

Is there a parser which allows me to read a gtf (or bed) file, select the lines containing the identifiers I request, and writing down the results to a new gtf (bed) file?

I can code a simple parser, but if a solution exists already (which is very likely..) I am interested. I am coding in R currently, but a Python script would be fine too.

Thanks for your advice

Answer 1

[Dan D]

Can't you just grep the GTF file for those gene/transcript names? You can output the list of names into a file, and then supply that file using the -f parameter, like this:

grep -f my_gene_and_transcript_list.txt genes.gtf > selected_genes.gtf

[cyril-cros]

You are perfectly correct, I was going for something needlessly complicated. Thanks a lot for your help.

[Dan D]

I'm glad it was that easy :)

[karl.stamm]

you might need the capital F flag to indicate exact matches only, or grep could find MAPK inside the line MAPK3.

Answer 2

[dimitrischat]

I got a similar question for this, because grep -f or grep -F doesnt work for me. I got a list of common genes between two cell types. Now i want to pick only the common genes from each condition ( each cell type ) from an excel file that contains

 id    baseMean   baseMeanA baseMeanB   foldChange  log2FoldChange  pval    padj    h6
   XAF1 34.9158621585   0   69.831724317    Inf        Inf        1.86E-15 1.13E-12 up

but 1) what if i want to grep only the (common)genes and some other condition , f.e the 4th one, baseMeanB 2) what if i want to grep all the line containing all conditions that follow each gene ( only the common ones ofcourse)

[jean.elbers]

You should perhaps make this a new question, but I would recommend awk. I unfortunately don't understand what you want, so perhaps you could give more detail for your questions 1) and 2) in a new post.