Grape Pipeline

Fill in this form with your required settings and launch the Grape Pipeline.

This pipeline was built with Nextflow - for more information see the pipeline documentation.

Data Locations

Index File:

This file should contain information about your input files. Click here to see an example.

sample1	test1	data/test1_1.fastq.gz	fastq	FqRd1
  sample1	test1	data/test1_2.fastq.gz	fastq	FqRd2

Genome File:

Path of a FastA file containing your reference genome.

Annotation File:

Path of a GTF file containing your reference annotation.

Pipeline Configuration

Max Mismatches:

Number of mismatches that should be tolerated, per read.

Max Multimaps:

Maximum number of non-unique alignments allowed per read.

Sorting Method:

Pipeline Steps:

Mapping

Bigwig

Contig

Quantification

Add XS tag?

Yes No

Add the XS field required by Cufflinks/Stringtie to the genome BAM file.

SAM Readgroup Details

Platform:

Platform/technology used to produce the reads for the BAM @RG tag.

Library:

Sequencing library name for the BAM @RG tag.

Center name:

Name of sequencing center that produced the reads for the BAM @RG tag.

Description:

Description for the BAM @RG tag.