where to obtain hg19 reference transcriptome in gencode
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3 months ago
Josh ▴ 20

Hi, I want to use salmon to generate an index and later use it again to get a table of counts that I can use for differential expression analysis with the hg19 version. For the hg38 reference genome I have had no problem downloading and using the gencode files (transcriptome in fasta and gtf format: https://www.gencodegenes.org/human/).

However for hg19 I have a question, which gencode file to download to get the hg19 transcriptome? In the following link https://www.gencodegenes.org/human/release_19.html I only see the gtf file that I should use (Comprehensive gene annotation - CHR - It contains the comprehensive gene annotation on the reference chromosomes only - This is the main annotation file for most users). My doubt arises because in the hg38 version, a specific file appears in: Transcript sequences - CHR - Nucleotide sequences of all transcripts on the reference chromosomes - Fasta.

If you could help me, I would be very grateful!

hg19 salmon gencode • 394 views

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