Entering edit mode
3.4 years ago
whaiyu06
▴
80
I'm writing to ask for your help. I use the latest STARsolo to analysis the 10x genomics data(Single Cell 3' v3), and exit with the "Illegal instruction" error .But I can't pick out which parameter(s) is inappropriate. The command I used as follows:
STAR --runMode alignReads \
--runThreadN 16 --genomeDir $refgenome \
--readFilesIn B10X-5_S25_L004_R2_001.fastq B10X-5_S25_L004_R1_001.fastq \
--soloType CB_UMI_Simple \
--soloFeatures GeneFull \
--soloUMIlen 12 \
--soloCBwhitelist $whitelist \
--clipAdapterType CellRanger4 \
--outFilterScoreMin 30 \
--soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts \
--soloUMIfiltering MultiGeneUMI_CR \
--soloUMIdedup 1MM_CR \
--soloCellFilter EmptyDrops_CR \
--outFileNamePrefix ./B10X-5
Thanks for your suggestions.
I ran the code without
--clipAdapterType CellRanger4
and added the--soloBarcodeReadLength 0
, then the output is correct.However, it doesn't work when only added the--soloBarcodeReadLength 0
. So the issue is the--clipAdapterType CellRanger4
, and I haven't settled.hello, what whitelist and refgenome did you used please ? could u share the link to download these files