sam-xlate to convert genomic coordinates

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Vitor Aguiar

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Dec 28, 2020, 9:46:26 AM12/28/20

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Hi all,

does anyone have experience with the sam-xlate tool to convert genomic to transcriptomic coordinates? It is recommended in the Salmon documentation since the early versions, but the project looks rather abandoned on github, it that correct?

I want to give it a shot, but I want to generate my own bed file from a GTF and I can't understand the example bed file. It resembles a UCSC reFlat table, but with a different order of columns, including end before start column, and apparently relative instead of absolute positions.

This is the example BED:

https://raw.githubusercontent.com/mozack/ubu/master/src/test/java/edu/unc/bioinf/ubu/sam/testdata/unc_hg19.bed

Can anyone help?

Thank you,

Vitor

Vitor Aguiar

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Jan 12, 2021, 3:37:00 PM1/12/21

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For those interested on this topic,

the file format is BED12. I was able to convert a GTF to BED12, and run sam-xlate. However, I'm still not confident with the expression estimates I'm getting from the sam-xlate BAM (with Salmon).