isolating genomic sequence based on RNAseq data
using RNAseq data I have the coordinates of 5p end of all expressed transcripts and I want to get the the sequence of that site (5p end) together with flanking area (5 nucleotide upstream and downstream) but at the genomic level (not RNA). the main problem is upstream of 5p end (beginning of 5pUTR) since that part is not present in transcriptome.
do you know how to get the sequence of 5p end (which is one nucleotide) together with 5 nucleotide upstream and downstream of that at the genomic level. in total the sequence for every gene would have 11 nucleotide length.
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alireza346 •
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If you have the genomic coordinates of all 5' ends, you should be able to use
awkto create a bed file with the start (pos - 5) and end (pos + 5) positions (width=11) for each transcript and then use that to extract sequences from the reference genome.