Do you guys know how to use net file format?

[thejustpark]

Hello experts,

I am trying to obtain human genes that overlap my mouse lncRNAs in human-mouse pairwise alignment.
For this purpose, I have been looking at mouse-human pairwise alignment in net format, but I can't fully understand what to do.

Is there no tool that can take in a net-formatted pairwise alignment and a bed file with genes of my interest in one species and spit out their counterparts for the other species based on the net file? I thought there should be such tools, but couldn't find one. And now I can't believe there is none for this purpose.

If you know how to do this, or know of tools for this, please let me know.

Thanks,

[dpryan]

I have no clue what the "net" format is, you'd need to provide a link. The easier route would be to make a GTF file of mouse lncRNAs and then use liftOver (or the online version from UCSC) to convert those to human coordinates. Then you have a single coordinate system to work and can simply subset your human annotation file with whatever tools you want (I'd suggest making a GRanges object in R out of things and just using its subset functions...that'd be quick and easy enough).