Closed dmiyagi closed 5 years ago
It's probably helpful if I leave this here as well slamdunk all -r /path/to/hg38.fa -b /path/to/3utr.bed -o /path/to/slamseq/ -m -n 100 --multiTCStringency /path/to/sampleInfo.tsv
and slamdunk all -r /path/to/hg38.fa -b /path/to/3utr.bed -o /path/to/slamseq/ -m -n 100 -mts /path/to/sampleInfo.tsv
Hi @dmiyagi
yes you are correct, the -c
flag replaces the -mts
flag in newer versions of Slamdunk. With -mts
the conversion threshold to call a read as TCRead
was hard-coded to 2 T>C conversions, with the new -c
flag you can dynamically define this threshold on your own. So indeed, setting -c 2
is equivalent to the previous -mts
flag.
Hi again t-neumann,
Thanks for answering my previous questions. I am trying to rerun slamdunk all with the -mts flag; however, I keep running into this error:
I noticed that in the explanation it doesn't have
-mts
but rather has-c CONVERSIONTHRESHOLD
I thought this might mean that I'm using an older version of slamdunk so I reinstalled/updated it and am still having this issue. It should be noted that I am not using the-t
parameter in my code. I also tried--multiTCStringency
and gotusage: slamdunk [-h] [--version] {map,filter,snp,count,all} ... slamdunk: error: unrecognized arguments: --multiTCStringency
. Any suggestions? is the-c
flag equivalent to the-mts
flag if I set it to-c 2
? Thanks!