gravatar for from the mountains

2 hours ago by

United States

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?



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