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alexdobin / STAR

RNA-seq aligner

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--soloStrand not working

Yenaled opened this issue · comments

commented

I am getting identical output whether I set it to Forward, Reverse, or Unstranded

STAR --outSAMattributes NH HI AS nM NM CR UR MD vA vG vW --waspOutputMode SAMtag --varVCFfile hybrid.vcf --genomeDir star_mm10_index --runThreadN 14 --readFilesCommand zcat --soloType CB_UMI_Simple --soloCBwhitelist None --soloBarcodeMate 1 --clip5pNbases 26 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 10 --soloUMIdedup Exact --soloUMIfiltering MultiGeneUMI_All --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --soloFeatures Gene GeneFull SJ --soloStrand Forward --outSAMattrRGline ID:Doxtitration1 SM:Doxtitration1 --outFileNamePrefix out_dir/ --readFilesIn R1.fastq.gz R2.fastq.gz

If I change --soloStrand, nothing is different.

commented

Closing this issue: The alignment (BAM file, alignment statistics, etc.) will remain unchanged regardless of --soloStrand option. However, the actual quantifications in the Solo.out directory will be affect.