Question: Creating Bed File For Lncrna Using Gencode Gtf File
1
gravatar for J.F.Jiang
6.0 years ago by
J.F.Jiang750
China
J.F.Jiang750 wrote:

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?

bedtools bed • 2.5k views
ADD COMMENTlink modified 6.0 years ago by biorepine1.4k • written 6.0 years ago by J.F.Jiang750

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

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by PoGibas4.8k
0
gravatar for biorepine
6.0 years ago by
biorepine1.4k
Spain
biorepine1.4k wrote:

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

ADD COMMENTlink written 6.0 years ago by biorepine1.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 896 users visited in the last hour