I am working on human cancer data and wanted to extract sequences from the human genome for analyzing SNPs. For that, I am trying to fetch exon start and end positions for the human genome build GRCh37. I used ucsc genome browser to download this data (using known Gene table)
The data has the same values for cds start and cds end. I am confused as to why this is the case, as cds is for coding region. Should I ignore this and go use exon start and end positions?
Any help is highly appreciated!
Thanks!
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written
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mlank001 •
Answer: This gene doesn't have normal usual structure as it is a long non-coding RNA (transcribed_unprocessed_pseudogene).
Explanation: In UCSC browser find gene name: DDX11L1.
curl -s "ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_21/gencode.v21.annotation.gtf.gz" |
gunzip -c |
tr -d ';"' |
awk '($3=="gene" && $18=="DDX11L1") {print $14}'
transcribed_unprocessed_pseudogene
Got it! thanks a lot! I appreciate it..
So this means I should indeed be looking at the cds Start and end positions for extracting the reference genome sequence to be translated.
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written
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mlank001 •
It depends. Are you interested only in protein coding genes? If so, check genecode genes, you can download list of all the protein coding genes (start end positions for gene/transcript/UTR/exon/CDS and genomic or translated fasta sequences).
In general, CDS start-end, they are noncoding transcripts
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Please post example of "
The data has the same values for cds start and cds end".Here is the example of one entry:
If you look at the 6th and 7th columns (cdsStart and cdsEnd), the values are the same. I am confused as to why that's the case.