Snakemake and STARsolo

0

Hello everyone,

I started a scRNA-seq project recently.

I wrote a snakemake script for the mapping part with STARsolo.

SAMPLES, = glob_wildcards("Data/Raw/{sample}_L001_R1.fastq.gz")

rule StarSolo:
    input:
        R1L1 = "Data/Raw/{sample}_L001_R1.fastq.gz",
        R1L2 = "Data/Raw/{sample}_L002_R1.fastq.gz",
        R2L1 = "Data/Raw/{sample}_L001_R2.fastq.gz",
        R2L2 = "Data/Raw/{sample}_L002_R2.fastq.gz"
    threads:
        8
    shell:
        'STAR --runThreadN {threads} '
        '--genomeDir /Genome/Human/GRCh38/ '
        '--readFilesIn {input.R1L1},{input.R1L2} {input.R2L1},{input.R2L2} '
        '--readFilesCommand gunzip -c '
        '--soloType CB_UMI_Simple '
        '--soloCBwhitelist 3M-february-2018.txt '
        '--soloCBlen 16 '
        '--soloUMIstart 17 '
        '--soloUMIlen 12 '

I obtained this error message:

Building DAG of jobs...
WildcardError in line 11 of /script/Snakefile4:
Wildcards in input files cannot be determined from output files:
'sample'

Where is the problem ? Line 11 is rule StarSolo.

Thank you for your help.


scRNA-seq


snakemake


Mapping


STARsolo

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