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STAR solo adapter sequences all A's after 31 bp #2214

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mohammedmsk opened this issue Sep 16, 2024 · 0 comments
Open

STAR solo adapter sequences all A's after 31 bp #2214

mohammedmsk opened this issue Sep 16, 2024 · 0 comments

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@mohammedmsk
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Hello Alex,

I am trying to run STARsolo on a special scRNA-seq library. My command is as below:

STAR
--runThreadN 6
--readFilesCommand zcat
--genomeDir /share/scratch/mohammed/references/star_v2.7.11b_Ensembl_GRCh37
--outFileNamePrefix star_output_6_subsample/test_out.STAR.
--readFilesIn subsample.NoUser_S5_R2_001.fastq.gz subsample.NoUser_S5_R1_001.fastq.gz
--soloType CB_UMI_Complex
--soloCBmatchWLtype 1MM
--soloCBwhitelist /share/flexomics/DGE/Reference/barcode_files/Barcode_1M_whitelist.txt
--soloAdapterSequence
AGAAAAGCACCGATT AGAATAATGACCAGC AGAAACATCAGCAC AGAATCAGCCAATTGG AGAAATACAGCCCTT
AGAAAGCCCAAGACAA AGAATCGTAAGCATCC AGAAAGTGACTGGTTC AGAATTAGCCTTCG AGAATTCCATATCCG
--soloCBposition 0_0_3_0
--soloUMIposition 3_0_3_9
--outSAMtype BAM SortedByCoordinate
--quantMode TranscriptomeSAM GeneCounts

my Cell Barcodes are pretty long and I think STARsolo is not reading anything beyond 31 bp. Below is what I am getting as barcodes:
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGGAAACGTTTGTAGGAGAAACATCAGCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGGAAACGTTTGTAGGAGAATTAGCCTTCG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGGAAAGGTCAGACTTAGAAACATCAGCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGGAAAGGTCAGACTTAGAATTAGCCTTCG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTGGAAACGTTTGTAGGAGAAACATCAGCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTGGAAACGTTTGTAGGAGAATTAGCCTTCG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTGGAAAGGTCAGACTTAGAAACATCAGCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTGGAAAGGTCAGACTTAGAATTAGCCTTCG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGGAAACGTTTGTAGGAGAAACATCAGCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGGAAACGTTTGTAGGAGAATTAGCCTTCG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGGAAAGGTCAGACTTAGAAACATCAGCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGGAAAGGTCAGACTTAGAATTAGCCTTCG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGGAAACGTTTGTAGGAGAAACATCAGCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGGAAACGTTTGTAGGAGAATTAGCCTTCG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGGAAAGGTCAGACTTAGAAACATCAGCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGGAAAGGTCAGACTTAGAATTAGCCTTCG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGGAAAAAACGTCACGAAGAAACATCAGCAC

Am I missing anything or there is an intended limitation or bug in the tool?

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