STARsolo read1 length greater than cell barcode length and UMI length

Question

[from the mountains]

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 ID=@... 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?

[GenoMax]

Untested but see if it works. Feed your reads into STARsolo by trying this:

reformat.sh in=R1.fq.gz out=stdout.fq.gz forcetrimleft=28 | pipe to your command. Set $barcode_read to read from STDIN.