XLOCs vs. TCONs while identifying LNCRNAs

[Blum, Roy]

Dear Steve Heitner,

I hope you are well,

I have a question regarding file formats that I hope you may be able to assist me with. 

I currently ran a cuffdiff analysis using a GTF file that I composed for LNC-RNAs. 

The GTF file contains both TCONS and XLOC annotations. 

I am then focusing on the cuffdiff output file "gene_exp.diff" and see the results for deferentially expressed non-coding genes. In the gene_exp.diff I get the report for all the so called 'non-coding genes' (in holds all the XLOCs), while in the isoform_exp.diff file i get the report for all the transcripts (it holds all the TCONs).
In column "D" of the gene_exp.diff I get the coordinates for each XLOC position. 

My question is as follows: 

I would like to use the original GTF table I created for LNCRNAs (which is basically a subtracted file of the original merge.gtf file I've got after running cuffmerge) - for plotting the n=LNCRNAs on IGB. 

However, when I do so - loading my GTF file - IGB presents the TCONs and not the XLOCs. 

Is there a way to make IGB to present XLOCs instead? 

In addition, I went through the steps of converting GTF into 12 column BED file using the UCSC table browser.
Once again, I am getting a bed file that holds all the TCONs but not the XLOCs. (I should note that a proper BED file would become important for me in further downstream analysis which will be referring to the promoter of the newly discovered LNCRNA genes, etc..) 

In case I would like to refer to the non-coding genes (as oppose to non-coding transcripts) - shouldn't I reefer to the XLOCs instead of the TCONs ? Is there a proper way to refer to XLOCs in this procedure? 

I would really appreciate getting your input in case you could assist me with this matter.  

Thanks a lot and good day, 

Roy
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Roy Blum, Ph.D.
Senior Research Scientist
Laura and Issac Perlmutter Cancer Center
New York University Langone Medical Center
552 First Ave. Smilow 2106

New York, NY, 10016
Mob:   +1 (646)-716-2875
Lab:    +1 (212)-263-2327
http://blumroy.googlepages.com

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[Brian Lee]

Dear Roy,

Thank you for using the UCSC Genome Browser and your question about attempting to uniquely format output of results from the Table Browser at UCSC and at the Integrated Genome Browser.

Thank you also for reviewing our archived mailing list to investigate your inquiry, I am assuming you may be referencing Steve's response to a user named Aishwarya about detecting novel lncRNA: https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!searchin/genome/Aishwarya

Perhaps a solution would be to use some UNIX command line operations to swap the terms in your input files, there is no simple Browser tool to solve your problem. Unfortunately, overall your question is beyond the scope of this mailing list, I highly recommend instead posting your question to the Biostars Bioinformatics forum, https://www.biostars.org/. At that site there may be other users who have been in a similar situation and who have used some command line scripts to provide the kind of final formats you are desiring.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UCSC Genome Bioinformatics Group

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