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PeteHaitch / methtuple

methtuple is a methylation caller for methylation events that co-occur on the same DNA fragment from high-throughput bisulfite sequencing data, such as methylC-seq.
MIT License
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More options for run_comethylation.sh #78

Closed PeteHaitch closed 10 years ago

PeteHaitch commented 10 years ago

In particular, the ability to pass TMP_DIR and VALIDATION_STRINGENCY to SortSam.

PeteHaitch commented 10 years ago

Update run_comethylation.sh to use samtools rather than Picard's SortSam; samtools sort -n does sort read_1 before read_2 provided it is v0.1.19 and not v0.1.18.