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Old 10-28-2011, 06:29 AM   #1
jhb1980
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Location: Switzerland

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Default Combining *.gtf files?

Hi,

I was wondering if anyone can point me towards a way to combine lines of one *gtf file with another *.gtf file...? Specifically, I would like to extract certain genes from the latest Ensembl mouse *.gtf and combine them with the current UCSC RefGenes *gtf.

I thought I'd get the lines of interest by a simple 'grep "my_gene_id"' form the Ensembl file. I'm not quite sure though what the best way to concatenate / sort the merged file would be, and if there may be other problems with this (e.g. overlapping exons of Ensembl and UCSC transcripts).

Any lead on this would be great!

Thank you,

Jan
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Old 10-31-2011, 08:55 AM   #2
jhb1980
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Default

Ah - found "gffread" in the Cufflinks package.... Works a blast.
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Old 11-01-2011, 01:43 AM   #3
arvid
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Default

BEDTools are quite useful for GFF/GTF as well, especially if you want to check overlaps etc. between files...
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