spikeIn sampe scaling factor calculation discrepenses about snakepipes HOT 2 CLOSED

Hi,
the default spikein_bin_size for calculating scaling factors from spikein genome is 1000 . This should be visible in the workflow config.yaml in the output folder.

In the first commandline you pasted, I've noticed you are passing host bam files to calculate spikein size factors. Then you're citing size factors from a file, in which they appear to be calculated on spikein bam files. Could you revisit that?

If you run snakePipes with --verbose, full shell commands will be returned in the log file. You can then see the full multiBamSummary command with all the parameters passed. Would that be helpful?

Best,

Katarzyna

from snakepipes.

In the first commandline you pasted, I've noticed you are passing host bam files to calculate spikein size factors. Then you're citing size factors from a file, in which they appear to be calculated on spikein bam files. Could you revisit that?

that was a typo from my side, I will come back after testing a few things

from snakepipes.