I am trying out STARsolo (STAR 2.7.3a) for the first time and wondering if i can side-step an additional trimming step. my reads are sequenced at 2x150 and from 10X libraries, and normally when i run through cellranger it ignores the bases after cell barcode and UMI. I can also set my desired R2 length with --r2-length
without an extra trimming step.
Any such luck with STARsolo?
my script is:
soloCBstart=1
soloCBlen=16
soloUMIstart=17
soloUMIlen=12
STAR --genomeDir $index
--sjdbGTFfile $gtf
--readFilesIn $cdna_read $barcode_read
--runThreadN $threads
--twopassMode Basic
--outWigType bedGraph
--outSAMtype BAM SortedByCoordinate
--readFilesCommand zcat
--runDirPerm All_RWX
--outFileNamePrefix $prefix $seq_center
--soloType Droplet
--soloCBstart $soloCBstart --soloCBlen $soloCBlen
--soloUMIstart $soloUMIstart --soloUMIlen $soloUMIlen
--soloCBwhitelist $whitelist
my error is:
EXITING because of FATAL ERROR in input read file: the total length of barcode sequence is 150 not equal to expected 28
Read [email protected] 1 N 0 Sequence=...
SOLUTION: make sure that the barcode read is the last file in --readFilesIn , and check that it has the correct formatting
If UMI+CB length is not equal to the barcode read length, specify barcode read length with --soloBarcodeReadLength
Adding --soloBarcodeReadLength 150 did not help the situation. can i run starsolo without trimming?