Creating Bed File For Lncrna Using Gencode Gtf File

Question

[J.F.Jiang]

Hi all,

I want to get the bed file of lncRNA based on GENCODE GTF file

I download the file "gencode.v16.long_noncoding_RNAs.gtf.gz", and extract the chr, start, end info from the file, then I use mergeBed to merge those overlapped lncRNA, am I correct? Since I know we can merge the exon genomic position using this kind of method

While for lncRNA I am not so sure, and is there any place already offering such kind of bed files?

actually, we should got 22444 Long non-coding RNA loci transcripts, however only 11817 genomic regions after merging process.

Anyone knows the answer, could you give me some help?

[PoGibas]

There are 22444 transcripts without merging, I don't see where's the problem.

Answer 1

[biorepine]

I answer the same question before. Hope this helps How To Convert Gencode Gtf Into Bed Format ?