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?
1 answer
I answer the same question before. Hope this helps How To Convert Gencode Gtf Into Bed Format ?
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There are 22444 transcripts without merging, I don't see where's the problem.