A Basic question regarding lncRNA identification pipeline.

Question

[rajeev.vikram]

Hi,

I have been analyzing RNA-Seq data sets of some Breast cancer cell lines to create a high confidence list of expressed lncRNAs. However as, I am new to NGS, I cannot figure out how do I filter out the known Expressed gene/protein coding transcripts from my annotation file after cufflinks assembly? Are there any specific tools to do the filtering? If anyone could help me regarding this, I will really appreciate your help.

Thanks

R

Answer 1

[GouthamAtla]

http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/

Answer 2

[rajeev.vikram]

Thanks, but my question is slightly different, , basically, after top-hat assembly with bowtie2 , I Used RABT assembly in cufflinks and then merged all transcripts (elegant= gtf file of annotated transcripts), then did cuffmerge of the replicates. After running cuffcompare with r- given as annotated gencode assembly, I got the transfrags identified with diff signs (=, c x etc.) Now I want to filter out all transfrags of ‘i’, ‘j’, ‘o’, ‘u’ and ‘x’ option, while making an extra file of known lncRNAs (by matching with bodymap annotated lncRNA.gtf). I am curious if I can do all that in command line in one comment, something like:

awk ‘$22 ~ /j,i,o,u,x/ { print }’..