five prime paired end star solo settings #1366
Description
Hi, I am trying figure out what settings to use in order for star solo to most closely match the outputs for cell ranger 5xx for 10x 5' paired end 150bp reads. I am currently trying the following, but the results are totally off in the gene/filtered/.. outputs.
STAR \
--genomeDir ./refdata-gex-GRCh38-STAR/ \
--readFilesIn $(echo my_files/*R2*fastq.gz | sed 's/ /,/g') $(echo my_files/*R1*fastq.gz | sed 's/ /,/g') \
--readFilesCommand zcat \
--soloFeatures Gene SJ GeneFull \
--runThreadN 16 \
--soloType CB_UMI_Simple \
--soloCBwhitelist ./whitelists/v2_737K-august-2016.txt \
--outFileNamePrefix "test." \
--outFilterScoreMin 30 \
--soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts \
--soloUMIfiltering MultiGeneUMI_CR \
--soloUMIdedup 1MM_CR \
--soloCellFilter EmptyDrops_CR \
--soloBarcodeMate 1 \
--clip5pNbases 39 0 \
--soloCBstart 1 \
--soloCBlen 16 \
--soloUMIstart 17 \
--soloUMIlen 10 \
--outSAMtype BAM Unsorted
Also , to note:
if I include Velocyto in the --soloFeatures I get a seg fault.
Thanks!
Jeffrey