Question: Creating Bed File For Lncrna Using Gencode Gtf File
gravatar for J.F.Jiang
6.8 years ago by
J.F.Jiang800 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 • 2.8k views
ADD COMMENTlink modified 6.8 years ago by biorepine1.4k • written 6.8 years ago by J.F.Jiang800

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

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by PoGibas4.8k
gravatar for biorepine
6.8 years ago by
biorepine1.4k wrote:

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

ADD COMMENTlink written 6.8 years ago by biorepine1.4k
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