Switch genomic coordinates to transcriptomic coordinates
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5.3 years ago
james.lloyd ▴ 100

I have a list of start and stop positions of a feature corresponding to a genome. The GTF annotation of this was generated in house. I have since made a transcriptomic fasta file from the genome fasta and the custom GTF. I would like to use a tool that looks at these features in the transcriptome but I have only the coordinates in the genome (transcript_id, chr, strand, start and stop) so is there any tool that can convert these features into one for the transcriptome fasta file (transcript_id, start and stop)? If there is a way to do it in bash, python or R, that would also be useful!

Many thanks in advance.

RNA-Seq fasta coordinates gene • 2.0k views
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5.3 years ago
slw287r ▴ 120

You can use the following two great tools:

Mutalyzer

TransVar

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