converting TCONS entries into XLOC values

Question

[mukundramakrishnan]

Hello All, I am looking for a way by which it is possible to display XLOC values instead TCONS values when I load my gtf file on to the IGV genome viewer. Thanks in advance. Best, Mukund

[Satyajeet Khare]

Hi Mukund,

Which files are you uploading? Are you uploading transcript.gtf output from Cufflinks output? The XLOC ids denote genes whereas TCONS ids denote transcripts. So if you replace TCONS id with corresponding XLOC ids, all transcripts will get same label.

[mukundramakrishnan]

Hi Satya, Thanks for your interest, I think my issue is one of visualization...Yes my output is a transcript.gtf (Cufflinks) file. When I load the gtf file on to the IGV viewer I would (somehow) like to replace the the TCONS values as they appear (in the display) by XLOC values. Is this possible? Best, Mukund

[Satyajeet Khare]

I use the gtf file to guide in tophat as well as cufflinks command, and I do not see either TCONS id or XLOC id in my transcript.gtf file. Instead I see the gene ids and transcript ids from my guide gtf (ENSEMBL, ENTREZ etc.). Can you please show your tophat and cufflinks commands? Do you run them without the guide gtf file?

Do you see XLOC ids as well as TCONS ids in your transcript.gtf file? If yes, did you try to simply replace the columns in spreadsheet and upload to IGV?

[mukundramakrishnan]

I see only the TCONS values...I have all the information in terms of the TCONS values and their corresponding gene id's or XLOC values as a fasta file, how do I use this information? How does one upload information from an excel file on to IGV?