Noncoding Rna Mapping
0
1
Entering edit mode
9.2 years ago
Honey ▴ 200

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

mapping file • 2.2k views
ADD COMMENT
2
Entering edit mode

It does sound like you want folks to do your assignment -- what have you tried already?

ADD REPLY

Login before adding your answer.

Traffic: 1160 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6