Mango fails at Stage 4 - bedtools merge not accepting piped unspecified stdin

[iwanttobeabadger]

Hi,

So when running Mango on the Heidari et al dataset I get a failure at stage 4 when it tries to extend peaks.

I've managed to fix this by editing the extendPeaks.R .... this change is necessary for bedtools v2.21.0 but I have not tested it on v.2.20.0 etc (but had previously managed to get the whole pipeline to run on an older system - not sure about versioning etc)

command = paste(bedtoolspath, " slop -i ",peaksfile, " -g ",bedtoolsgenome," -b ",peakslop,
" | ", bedtoolspath, " merge -i stdin -c 4 -o collapse > ",peaksfileslop,sep="")

This behaviour seems weird, but it could just be a bedtools feature/change, but it may be worth it to it specify directly.

HTH .... thanks,

[dphansti]

That is odd behavior and the first I have heard of it. I do not see that behavior with bedtools v2.24.0. I looked through the bedtools release notes as well and didn't see any mention of a change to this behavior. Can you share the error that you were getting?

Thanks.