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OSU-SRLab / MANTIS

Microsatellite Analysis for Normal-Tumor InStability
GNU General Public License v3.0
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Issue in runni #47

Closed YuvaraniThambidurai closed 5 years ago

YuvaraniThambidurai commented 5 years ago

Hi The Bed file generated from RepeatFinder is of length 3109671 lines. I tried to use this BED file for MANTIS but after running couple of hours, I often receive the message as Broken pipe. In all the condition I have used 3 threads as per your advice. Could u please help me in resolving this?

rbonneville commented 5 years ago

RepeatFinder finds all putative microsatellite regions in an entire genome. This BED file must be filtered with your desired capture region, for example:

bedtools intersect -a microsatellites.bed -b regions.bed -wa > microsatellites_filtered.bed