STAR reading command options --winAnchorMultimapNmax --outFilterMultimapNmax

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Ellen NM

May 22, 2023, 11:02:16 AMMay 22
to rna-star


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


Alexander Dobin

May 22, 2023, 3:50:04 PMMay 22
to rna-star
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.

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