Is having a hard time getting SAM files converted into sensible BED files – argh…
Is having a hard time getting SAM files converted into sensible BED files – argh getting so frustrated. Guess I'll have to convert what I did into a biostar question and see if someone knows what I'm doing wrong. Can't be that hard converting http://funpopgen.unige.ch/data/ceu60 SAM data set into BED files so that I can run FluxCapacitor…..
Embedded Link
CEU60 |
Citation: Stephen B. Montgomery, Micha Sammeth, Maria Gutierrez-Arcelus, Radoslaw P. Lach, Catherine Ingle, James Nisbett, Roderic Guigo, Emmanouil T. Dermitzakis. “Transcriptome genetics using s…
4 Replies to “Is having a hard time getting SAM files converted into sensible BED files – argh…”
Good luck. I'm not downloading 50 gigs to check it… : ) Are you using bedtools?
Good luck. I'm not downloading 50 gigs to check it… : ) Are you using bedtools?
Haha, the files are indeed pretty big…. I'm using bedtools + samtools indeed. It should be so easy… almost done writing the text for biostar, just have to re-run a few steps to make sure it really doesn't work
Haha, the files are indeed pretty big…. I'm using bedtools + samtools indeed. It should be so easy… almost done writing the text for biostar, just have to re-run a few steps to make sure it really doesn't work