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Old 09-11-2015, 09:17 AM   #1
Location: Munich

Join Date: Jul 2015
Posts: 14
Default Cufflinks: map transcripts_id to nearest_ref

I believe this is a very simple question, but since I am a scripting noob, I am completely lost:

In the merged.gtf (cuffmerge output), each transcript is assigned a TCONS_##### number. I have a list of differntially expressed isoforms with exactly these IDs and I am interested in the corresponding refGene annotations. This won't work for novel transcripts, sure but let's say I disregard them. Could anyone please instruct me on how to extract these numbers from the merged.gtf? I don't mind using R or grep or sed or awk, no matter what. I just need an idea where to start.

In brief: I have a list of TCONS numbers and I would like to extract the corresponding nearest_ref from this type of data:
chr1	Cufflinks	exon	943908	944581	.	+	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000016"; exon_number "14"; gene_name "SAMD11"; oId "NM_152486"; nearest_ref "NM_152486"; class_code "="; tss_id "TSS6"; p_id "P2";
Thanks a lot!

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