Penn SCAP-T Pipeline: Documentation
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Module: STATS
This module will print out the stats from BLAST, TRIM and either STAR or RUM. The stats will be tab delimited so they can be copy-pasted into an Excel table.
Usage:
ngs.sh stats [-v] modules sampleID
Input:
module specific
Output:
printing to console
Options:
-v - verbose printing of alignment stats (default: off).
modules - comma separated, ordered list of modules to include for stats (must not include spaces).
Prints stats for user-specified list of modules. The stats will be tab delimited so they can be copy-pasted into an Excel table. This will not write to the analysis.log file.