-mts flag

[dmiyagi]

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:

`usage: slamdunk all [-h] -r REFERENCEFILE -b BED [-fb FILTERBED] -o OUTPUTDIR
                    [-5 TRIM5] [-a MAXPOLYA] [-n TOPN] [-t THREADS] [-q] [-e]
                    [-m] [-mq MQ] [-mi IDENTITY] [-nm NM] [-mc COV] [-mv VAR]
                    [-c CONVERSIONTHRESHOLD] [-rl MAXLENGTH] [-mbq MINQUAL]
                    [-i SAMPLEINDEX] [-ss]
                    files [files ...]
slamdunk all: error: argument -t/--threads: invalid int value: 's'

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 got usage: 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!

[dmiyagi]

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

[t-neumann]

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.