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
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cyril-cros
You are perfectly correct, I was going for something needlessly complicated. Thanks a lot for your help.
you might need the capital F flag to indicate exact matches only, or grep could find MAPK inside the line MAPK3.
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)
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.
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