Paired-end RNAseq data processing workflow designed for execution on the BigPurple HPC. This version enables assembly of novel transcript isoforms. Primary software used: FastQC, Fastp, HISAT2, StringTie, MultiQC

public public 1yr ago 0 bookmarks
View Workflow
Report
rnaseq_pe_hisat2_stringtie_novel_transcripts
rnaseq_pe_hisat2_stringtie_novel_transcripts
View Workflow

RNAseq_PE_HISAT2_stringtie_novel_transcripts

This readme describes how to execute the snake make workflow for paired-end RNA-seq pre-processing (fastq -> feature counting) utilizing HISAT2 and Stringtie for alignment and gene/transcript lev

Code Snippets

41
42
shell: 
	'fastqc {input.fastq} -o {params}'
SnakeMake FastQC From line 41 of main/Snakefile 
58
59
shell:
	'fastp -w {threads} {params} -i {input.R1} -I {input.R2} -o {output.R1} -O {output.R2} --html {output.html} --json {output.json} 2> {log}'
SnakeMake fastp From line 58 of main/Snakefile 
72
73
74
75
76
77
	shell:
		'hisat2 {params} -p {threads} -x %s -1 {input.R1} -2 {input.R2} 2> {log} | samtools sort - -o alignment/{wildcards.sample}.bam -@ {threads}' % (genome)

rule count:
	input:
		bam = 'alignment/{sample}.bam'
SnakeMake SAMtools HISAT2 From line 72 of main/Snakefile 
84
85
86
87
88
89
90
91
	shell:
		'stringtie -p {threads} {params} -G %s -o {output.trans_counts} -l {wildcards.sample} -A {output.gene_counts} {input.bam}' % (GTF)

rule combine_gtf:
	input:
		trans_counts = expand('stringtie/{sample}.gtf' , sample = sample_ids)
	output:
		gtf_list = 'stringtie/merged.txt'
SnakeMake StringTie From line 84 of main/Snakefile 
92
93
shell:
	'ls stringtie/*.gtf > {output.gtf_list}'
SnakeMake From line 92 of main/Snakefile 
101
102
103
104
105
106
107
	shell:
		'stringtie --merge -p {threads} -G %s -o {output.merged_gtf} {input.gtf_list}' % (GTF)

rule count_2:
	input:
		bam = 'alignment/{sample}.bam',
		merged_gtf = 'stringtie/merged.gtf'
SnakeMake StringTie From line 101 of main/Snakefile 
113
114
shell:
	'stringtie -p {threads} {params} -G  {input.merged_gtf} -o {output.trans_counts} {input.bam}'
SnakeMake StringTie From line 113 of main/Snakefile 
123
124
shell:
	'prepDE.py -l 65 -i {input.str_dir} -g {output.gene_counts} -t {output.transcript_counts}'
SnakeMake From line 123 of main/Snakefile
ShowHide 4 more snippets with no or duplicated tags.

Login to post a comment if you would like to share your experience with this workflow.

Do you know this workflow well? If so, you can request seller status , and start supporting this workflow.

Free

Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/mgildea87/RNAseq_PE_HISAT2_stringtie_novel_transcripts
Name: rnaseq_pe_hisat2_stringtie_novel_transcripts
Version: 1
Badge:
workflow icon

Insert copied code into your website to add a link to this workflow.

Downloaded: 0
Copyright: Public Domain
License: None
  • Future updates

Related Workflows

psychip_snakemake
Show Details View Workflow
ENCODE pipeline for histone marks developed for the psychENCODE project
public

public

psychip pipeline is an improved version of the ENCODE pipeline for histone marks developed for the psychENCODE project. The o...
raw sequence reads Alignment Sequence alignment report macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
ncov_2
Show Details View Workflow
Near-real time tracking of SARS-CoV-2 in Connecticut
public

public

Repository containing scripts to perform near-real time tracking of SARS-CoV-2 in Connecticut using genomic data. This pipeli...
JSON nextclade Augur Biopython FOCUS Pandas Snakemake bs4 epiweeks geopy matplotlib numpy pycountry pycountry-convert uszipcode
Free
28
cellranger-snakemake-gke
Show Details View Workflow
snakemake workflow to run cellranger on a given bucket using gke.
public

public

A Snakemake workflow for running cellranger on a given bucket using Google Kubernetes Engine. The usage of this workflow ...
macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
atlas
Show Details View Workflow
ATLAS - Three commands to start analyzing your metagenome data
public

public

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
raw sequence reads Genome assembly Annotation track checkm2 gunc prodigal snakemake-wrapper-utils MEGAHIT Atlas BBMap Biopython BioRuby Bwa-mem2 cd-hit CheckM DAS Diamond eggNOG-mapper v2 MetaBAT 2 Minimap2 MMseqs MultiQC Pandas Picard pyfastx SAMtools SemiBin Snakemake SPAdes SqueezeMeta TADpole VAMB CONCOCT ete3 gtdbtk h5py networkx numpy plotly psutil utils metagenomics
Free
175
rna-seq-star-deseq2
Show Details View Workflow
RNA-seq workflow using STAR and DESeq2
public

public

This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
raw sequence reads Gene expression profiling ID list snakemake-wrapper-utils biomaRt PCAtools BiocParallel BWA Cutadapt DESeq2 GFFutils MultiQC Pandas SAMtools Snakemake STAR cli stringr tidyverse RNA-Seq
Free
41
dna-seq-gatk-variant-calling
Show Details View Workflow
This Snakemake pipeline implements the GATK best-practices workflow
public

public

This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
VCF raw sequence reads Variant calling genetic variants gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BWA FastQC MultiQC Pandas Picard SAMtools Snakemake Trimmomatic Variant Effect Predictor (VEP) common matplotlib numpy seaborn DNA
Free
57