nextflow run RNAseqPipe/main.nf -profile c2 --read "*_{1,2}.fq.gz" --designfile "design.file" --comparefile "compare.txt"
The SYSUCC-RNAseqPipe pipeline comes with documentation about the pipeline, found in the docs/ directory:
The pipeline allows you to choose between running either replicates or without replicates.
Choose between workflows by using --without_replicate or not(default) .
| Step | With replicates | without_replicate |
|---|---|---|
| Raw data QC | Fastp | Fastp |
| Align Reads | STAR | STAR |
| Alignment QC | Qualimap | Qualimap |
| Reads counting | RSEM | RSEM |
| Matrix collapses | DAtools | DAtools |
| Differential expression | DESeq2 | Poisson Test(DAtools) |
| Gene Set enrichment Analysis | GSEA | - |
| Summary Report | MultiQC | MultiQC |
design.txt
sampleInfor presents the experimental design of your data set, it is just like a design file of DESeq2 and EdgeR input.
Sample Type
P1003NA N
P1003TA T
P1162NA N
P1162TA T
P1408NA N
P1408TA T
P1527NA N
compare.txt
specify which group to compare in your differential expression analysis
T_vs_N
T and N are the identical strings as the Type column in design.txt.
--reads
suffix of your raw reads file. For example, *_{1,2}.fq.gz for paired end reads file sampleA_1.fq.gz and sampleA_2.fq.gz
--designfile
design file
--comparefile
compare file
--gene_gtf
gtf file for building your STAR index
--singleEnd
true when using a single End reads input, default false
--strand
true when using strand specific library , default false
--skip_qc
set ture if you are going to skip qc step
--without_replicate
set ture if your have no biological replicate.
*note: for no replicate mode, the compare file should be directly specified as SampleName_vs_SampleName have just been trimmed by read suffix string *
Content type
Image
Digest
Size
1.1 GB
Last updated
almost 8 years ago
docker pull likelet/rnaseqpipe