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Altius / hotspot2

Implementation of hotspot2 by Eric Rynes
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scripts/hsmerge.sh creates empty files #29

Closed brianpenghe closed 5 years ago

brianpenghe commented 5 years ago

I first called hotspots using this: hotspot2-2.1.1/scripts/hotspot2.sh -f 0.1 -F 0.1 -c chrom_sizes.bed -C center_sites.starch Sample.bam SampleOut/

Then I got Sample.hotspots.fdr0.1.starch

Then I tried to set fdr=0.05

hotspot2-2.1.1/scripts/hsmerge.sh -f 0.05 Sample.hotspots.fdr0.1.starch Sample.hotspots.fdr0.05.starch

Then I converted this starch to bed

unstarch Sample.hotspots.fdr0.05.starch > Sample.fdr0.05.bed

However, that bed file is empty. If I independently ran hotspot with default, the fdr0.05 is not empty.

So why did scripts/hsmerge.sh fail?

Thanks

erynes commented 5 years ago

It looks like you specified the wrong input file for hsmerge.sh. In addition to Sample.hotspots.fdr0.1.starch, hotspot2 should have created a much larger file called Sample.allcalls.starch. The latter is the necessary input file for hsmerge.sh. If you re-run hsmerge.sh with Sample.allcalls.starch as the input file, it should work fine. Please let us know if it doesn't.

brianpenghe commented 5 years ago

Thanks!