gtf file reverse complement coordinates

[lwhitmore]

Hey All, I have a question about chromosomal coordinates and Htseq. If I wanted to see if reads mapped to the chromosome location 4544400:4559600 on chromosome 1 the gtf line for this would be
chr1 piRNAbank 4544400 4559600 15200 + . gene_id "piRNAcluster_1"

Now lets say I wanted to see if the reads I have map to this same region on the reverse complement or - strand would the gtf entry be
chr1 piRNAbank 4544400 4559600 15200 - . gene_id "piRNAcluster_1"
or would I have to get different coordinates for the reverse complement?
Hopefully this makes sense and thanks for the help!
Leanne

[dpryan]

What you have is correct, you just switch the strand column (from + to -) to denote the other strand.

[lwhitmore]

Great thank you!

[lwhitmore]

By any chance does anyone know if there is a way to convert mm9 chromosome coordinates to mm10 genome coordinates?

Thanks
Leanne

[GenoMax]

By any chance does anyone know if there is a way to convert mm9 chromosome coordinates to mm10 genome coordinates?

Thanks
Leanne

Use liftOver utility at UCSC: https://genome.ucsc.edu/cgi-bin/hgLiftOver