I had some extremely long processing times (>24 hours) that led me to explore ways to speed up processing.
I found that the command --no-temp-splicesite drastically decreases the processing time. What is the consequence of using --no-temp-splicesite? I am primarily running hisat2 on human samples for DEG and differential alternative splicing events.
Hello,
I had some extremely long processing times (>24 hours) that led me to explore ways to speed up processing.
I found that the command --no-temp-splicesite drastically decreases the processing time. What is the consequence of using --no-temp-splicesite? I am primarily running hisat2 on human samples for DEG and differential alternative splicing events.
Below is the command that I am running:
hisat2 -p 30 -x ${REF} -1 ${SAMPLE_NAME}_R1.fastq.gz -2 ${SAMPLE_NAME}_R2.fastq.gz \ -t \ -S ${SAMPLE_NAME}.temp.sam \ --no-temp-splicesite \ --downstream-transcriptome-assembly \ --rna-strandness RF \ 2> ${SAMPLE_NAME}.hisat2.log
Thank you