Figure out how to reduce processing time - Githubissues

NAL-i5K / NAL_RNA_seq_annotation_pipeline

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Figure out how to reduce processing time #31

Closed mpoelchau closed 4 years ago

mpoelchau commented 4 years ago

Perhaps perform alignment steps (Hisat) in parallel.
use different queue

HsiuKangHuang commented 4 years ago

Samtools and Hisat are able to run with multiple threads, which can reduce the processing time.

Hisat use option "-p" https://ccb.jhu.edu/software/hisat2/manual.shtml#performance-tuning
Samtools (both view and sort) use option "-@" http://www.htslib.org/doc/1.6/samtools.html

mpoelchau commented 4 years ago

The number of threads can be specified in sbatch.sh (https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/blob/update-rnannot/rnannot/sbatch.sh#L4)