KisSplice2RefTranscriptome runtime length

Question

[TrentGenomics]

Hi,

I'm currently running kissplice2reftranscriptome to predict the impact of SNPs using paired-end reads from 4 samples (8 reads files total, ~45 million bp per file, ~14 gigabytes per file). My 'mergeSNPs.tsv' file is currently ~ 25 megabytes after 24 hrs.

What length of runtime should I be expecting? KisSplice took between 3-4 days to run.

Any info would be great. I feel like I may in for the long-haul! Thanks.

Answer 1

[TrentGenomics]

An update:

Finished writing the mainOutput.tsv after ~ 2 days. Still writing the lowQueryCoverageOutput.tsv.