STAR reading command options --winAnchorMultimapNmax --outFilterMultimapNmax

[Ellen NM]

Hi, 

I'm new to STAR and am trying to prepare alignments to run with TEtranscripts.

I specify -winAnchorMultimapNmax 100 --outFilterMultimapNmax -100 in my command.

The command runs but these options don't appear as user derived parameters in the Log.out file. 

I am running STAR 2.7.8a.

Command below:

STAR --runThreadN 1 \

--genomeDir /path/to/genome \

--readFilesIn /path/to/.fastq \

--outSAMtype BAM SortedByCoordinate \

--quantMode GeneCounts \

--outFileNamePrefix /path/to/output \

--winAnchorMultimapNmax 100 \

--outFilterMultimapNmax 100 \

Output in Log.out:

##### Final user re-defined parameters-----------------:

runThreadN                        1

genomeDir                         /path/to/genome

readFilesIn                       /path/to/.fastq

outSAMtype                        BAM   SortedByCoordinate

quantMode                         GeneCounts

Should they appear in the Log.out file? If so, do you have any suggestions about why the above command is incorrect?

Many thanks

Ellen

[Alexander Dobin]

Hi Ellen,

yes, all parameters should appear in the Log.out file. It's always a good idea to check the Log.out file for correctness of the parameters.

In this case there is likely a problem with command line formatting, such as an extra space after --quantMode GeneCounts \
since STAR does not see the rest of the command line.

Cheers

Alex