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Raw fastq files uploaded to Synapse by researcher in a folder with name format
experiment_name_rnaseq_fastq_date
. No white space should be present in the filenames (all filenames should have_
for whitespaces.All experiment and sample related annotations need to be added on Synapse before processing can start. This is a required step so that a sample sheet can be generated to trigger the processing workflow
The sample sheet should contain the following information in the following format (saved as a
.csv
files file):
sample | single_end | fastq_1 | fastq_2 | strandedness | |
sample_id_1Synapse specimenID | 0 (1 if paired-end) | synID | synID | reverse or forward | sample_id_2
The files are pulled into NextFlow workflow setup and processed using the following versions of software:
Code Block BEDTOOLS_GENOMECOV: bedtools: 2.30.0 CAT_FASTQ: cat: 8.3 CUSTOM_DUMPSOFTWAREVERSIONS: python: 3.9.5 yaml: 5.4.1 DESEQ2_QC_STAR_SALMON: bioconductor-deseq2: 1.28.0 r-base: 4.0.3 DUPRADAR: bioconductor-dupradar: 1.18.0 r-base: 4.0.2 FASTQC: fastqc: 0.11.9 GET_CHROM_SIZES: samtools: 1.1 GTF_GENE_FILTER: python: 3.8.3 PICARD_MARKDUPLICATES: picard: 2.25.7 PRESEQ_LCEXTRAP: preseq: 3.1.1 QUALIMAP_RNASEQ: qualimap: 2.2.2-dev RSEM_PREPAREREFERENCE_TRANSCRIPTS: rsem: 1.3.1 star: 2.7.6a RSEQC_BAMSTAT: rseqc: 3.0.1 RSEQC_INFEREXPERIMENT: rseqc: 3.0.1 RSEQC_INNERDISTANCE: rseqc: 3.0.1 RSEQC_JUNCTIONANNOTATION: rseqc: 3.0.1 RSEQC_JUNCTIONSATURATION: rseqc: 3.0.1 RSEQC_READDISTRIBUTION: rseqc: 3.0.1 RSEQC_READDUPLICATION: rseqc: 3.0.1 SALMON_QUANT: salmon: 1.5.2 SALMON_SE_GENE: bioconductor-summarizedexperiment: 1.20.0 r-base: 4.0.3 SALMON_TX2GENE: python: 3.8.3 SALMON_TXIMPORT: bioconductor-tximeta: 1.8.0 r-base: 4.0.3 SAMPLESHEET_CHECK: python: 3.8.3 SAMTOOLS_FLAGSTAT: samtools: 1.13 SAMTOOLS_IDXSTATS: samtools: 1.13 SAMTOOLS_INDEX: samtools: 1.13 SAMTOOLS_SORT: samtools: 1.13 SAMTOOLS_STATS: samtools: 1.13 STAR_ALIGN: star: 2.6.1d STRINGTIE: stringtie: 2.1.7 TRIMGALORE: cutadapt: 3.4 trimgalore: 0.6.7 UCSC_BEDCLIP: ucsc: 377 UCSC_BEDGRAPHTOBIGWIG: ucsc: 377 Workflow: Nextflow: 21.10.5 nf-core/rnaseq: '3.4'
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