I thought it will be better to start a new thread with this question, I was discussing one of the basic topic on this in another question.

It is suggested that for lincRNA expression Cabili et al (http://genesdev.cshlp.org/content/early/2011/09/02/gad.17446611.abstract) list may be used. However this - http://www.broadinstitute.org/genome_bio/human_lincrnas/?q=lincRNA_catalog has several such lincRNAs (I understand about TUCP_). My questions are-

1. Which one to choose - Do I combine lincRNas + Stringentset + 9 additional known lincRNA or just go with lincRNA_transcript.
2. Assuming that I have to use only lincRNAtranscript- I used its bed file to map my RNA-seq reads and find out DE? Now how would I get annotation from lincRNA_transcript GTF file. The later has several entries for same lincRNA, which coordinates from gtf file should be selected and how we can have one lincRNA per row. I am interested in already annotated lincRNAs at this time.

It may sound that I want folks to do my assignment but it is not correct After two days of my struggle and email to Broad guy proved to be unsuccessful. I am sure some one is using these files. This is also true for UCSC lincRNA files. Perhaps I am missing a simple point.

Thanks