Snakemake project for common mm10 reference files

public 1yr ago 0 bookmarks

View Workflow

Help improve this workflow!

This workflow has been published but could be further improved with some additional meta data:

Keyword(s) in categories input, output, operation, topic

You can help improve this workflow by suggesting the addition or removal of keywords, suggest changes and report issues, or request to become a maintainer of the Workflow .

This repository provides a Snakemake pipeline to download and transform mm10-related reference files that are used in bioinformatics workflows. Among the derivable files include:

UCSC genome FASTA
GENCODE GFFs/GTFs
salmon and kallisto indices
filtered versions of GENCODE (protein-coding, verified 3'-ends)
truncated versions of transcriptome annotations (used for 3'-end tag-based RNA-seq)

This serves as a record of data provenance.

Code Snippets

if (interactive()) {
  library(methods)
  Snakemake <- setClass(
    "Snakemake", 
    slots=c(
      input='list', 
      output='list',
      wildcards='list',
      threads='numeric'
    )
  )
  snakemake <- Snakemake(
      input=list(gtf="gencode.vM21.annotation.mRNA_ends_found.gtf.gz"),
      output=list(gtf="/fscratch/fanslerm/gencode.vM21.annotation.mRNA_ends_found.txcutr.w500.gtf",
                  fa="/fscratch/fanslerm/gencode.vM21.annotation.mRNA_ends_found.txcutr.w500.fa"),
      wildcards=list(width="500"),
      threads=1
  )
}

################################################################################
## Libraries and Parameters
################################################################################

library(txcutr)
library(BSgenome.Mmusculus.UCSC.mm10)
library(GenomicFeatures)

mm10 <- BSgenome.Mmusculus.UCSC.mm10

maxTxLength <- as.integer(snakemake@wildcards$width)

## set cores
BiocParallel::register(BiocParallel::MulticoreParam(snakemake@threads))

################################################################################
## Load Data, Truncate, and Export
################################################################################

txdb <- makeTxDbFromGFF(file=snakemake@input$gtf,
                        organism="Mus musculus",
                        taxonomyId=10090,
                        chrominfo=seqinfo(mm10))

txdb_result <- truncateTxome(txdb, maxTxLength)

exportGTF(txdb_result, snakemake@output$gtf)

exportFASTA(txdb_result, mm10, snakemake@output$fa)

R Snakemake BSgenome.Mmusculus.UCSC.mm10 txcutr From line 7 of scripts/txcutr_gtf.R

if (interactive()) {
  library(methods)
  Snakemake <- setClass(
    "Snakemake", 
    slots=c(
      input='list', 
      output='list', 
      wildcards='list',
      threads='numeric'
    )
  )
  snakemake <- Snakemake(
    input=list(),
    output=list(gtf="txdb.mm10.ensGene.txcutr.w{width}.gtf",
                fa="txdb.mm10.ensGene.txcutr.w{width}.fa"),
    wildcards=list(width="500"),
    threads=1
  )
}

################################################################################
## Libraries and Parameters
################################################################################

library(txcutr)
library(BSgenome.Mmusculus.UCSC.mm10)
library(TxDb.Mmusculus.UCSC.mm10.ensGene)

mm10 <- BSgenome.Mmusculus.UCSC.mm10
txdb <- TxDb.Mmusculus.UCSC.mm10.ensGene

maxTxLength <- as.integer(snakemake@wildcards$width)

## set cores
BiocParallel::register(BiocParallel::MulticoreParam(snakemake@threads))

################################################################################
## Truncate and Export
################################################################################

txdb_result <- truncateTxome(txdb, maxTxLength)

exportGTF(txdb_result, snakemake@output$gtf)

exportFASTA(txdb_result, mm10, snakemake@output$fa)

R Snakemake BSgenome.Mmusculus.UCSC.mm10 TxDb.Mmusculus.UCSC.mm10.ensGene txcutr From line 7 of scripts/txcutr_txdb_ensgene.R

shell:
    """
    wget -O {output} {params.url}
    """

SnakeMake From line 18 of master/Snakefile

shell:
    """
    wget -O- {params.url} | sort -k1,1 -k2,2n | bgzip > {output.bed}
    tabix {output.bed}
    wget -O- {params.url_tissue} | sort -k1,1 -k2,2n | bgzip > {output.bed_tissue}
    tabix {output.bed_tissue}
    """

SnakeMake tabix From line 33 of master/Snakefile

shell:
    """
    wget {params.url_base}{output.gff}
    wget {params.url_base}{output.gtf}
    wget {params.url_base}{output.fa}
    """

SnakeMake From line 50 of master/Snakefile

shell:
    """
    gzip -cd {input} | sed 's/|.*//' | pigz -p {threads} > {output}
    """

SnakeMake From line 65 of master/Snakefile

shell:
    """
    wget -qO - 'http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.fa.gz' |
    gunzip -c > {output}
    """

SnakeMake From line 73 of master/Snakefile

shell:
    """
    kallisto index -i {output} {input}
    """

SnakeMake kallisto From line 88 of master/Snakefile

shell:
    """
    gzip -cd {input} | awk '!( $0 ~ /^#/ )' | sort --parallel={threads} -S4G -k1,1 -k4,4n | bgzip -c > {output.gff}
    tabix {output.gff}
    """

SnakeMake tabix From line 100 of master/Snakefile

shell:
    """
    mysql --user=genome -N --host=genome-mysql.cse.ucsc.edu -A -D mm10 -e 'select name,name2 from refGene' > {output}
    """

SnakeMake From line 109 of master/Snakefile

shell:
    """
    gzip -cd {input} |
    awk '$0 !~ /mRNA_end_NF/' |
    bgzip -c > {output.gff}
    tabix {output.gff}
    """

SnakeMake tabix From line 120 of master/Snakefile

shell:
    """
    gzip -cd {input} |
    awk '$0 !~ /mRNA_end_NF/' |
    bgzip -c > {output.gtf}
    """

SnakeMake From line 133 of master/Snakefile

shell:
    """
    gzip -cd {input} |
    grep -v '^#' |
    gtfToGenePred /dev/stdin /dev/stdout |
    genePredToBed stdin {output}
    """

SnakeMake gtftogenepred From line 147 of master/Snakefile

shell:
    """
    gzip -cd {input} | awk -f scripts/gtf_tx2gene.awk > {output}
    """

SnakeMake From line 160 of master/Snakefile

shell:
    """
    wget -qO - 'https://github.com/morrislab/qapa/releases/download/v1.3.0/qapa_3utrs.gencode_VM22.mm10.bed.gz' |
    gunzip -c > {output}
    """

SnakeMake From line 168 of master/Snakefile

shell:
    """
    qapa fasta -f {input.fa} {input.bed} {output}
    """

SnakeMake QAPA From line 182 of master/Snakefile

shell:
    """
    salmon index -t {input} -i {output}
    """

SnakeMake Salmon From line 195 of master/Snakefile

shell:
    """
    grep "^>" {input.genome} | cut -d ' ' -f 1 > {params.decoy}
    sed -i.bak -e 's/>//g' {params.decoy}
    cat {input.qapa} {input.genome} > {params.fa}
    salmon index -t {params.fa} -d {params.decoy} -p {threads} -i {output}
    rm {params.decoy}
    rm {params.fa}
    """

SnakeMake Salmon From line 213 of master/Snakefile

shell:
    """
    mysql --user anonymous --host=martdb.ensembl.org --port=5316 -A ensembl_mart_{wildcards.version} \\
    -e "select stable_id_1023 as 'Gene stable ID', stable_id_1066 as 'Transcript stable ID', \\
    biotype_1020 as 'Gene type', biotype_1064 as 'Transcript type', \\
    display_label_1074 as 'Gene name' from mmusculus_gene_ensembl__transcript__main" \\
    > {output}
    """

SnakeMake From line 226 of master/Snakefile

script: "scripts/txcutr_txdb_ensgene.R"

SnakeMake From line 245 of master/Snakefile

script: "scripts/txcutr_gtf.R"

SnakeMake From line 259 of master/Snakefile

shell:
    """
    kallisto index -i {output} {input}
    """

SnakeMake kallisto From line 270 of master/Snakefile

ShowHide 15 more snippets with no or duplicated tags.

Comments

Support

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

Created: 1yr ago

Updated: 1yr ago

Maitainers: public

URL: https://github.com/mfansler/mm10-db

Name: mm10-db

Version: 1

Badge:

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

License: None

Keywords:

BSgenome.Mmusculus.UCSC.mm10 TxDb.Mmusculus.UCSC.mm10.ensGene tabix txcutr GenomicFeatures gtftogenepred kallisto QAPA Salmon Snakemake

Future updates

Related Workflows

psychip_snakemake — Show Details View Workflow

ENCODE pipeline for histone marks developed for the psychENCODE project

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

Near-real time tracking of SARS-CoV-2 in Connecticut

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

cellranger-snakemake-gke — Show Details View Workflow

snakemake workflow to run cellranger on a given bucket using gke.

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

ATLAS - Three commands to start analyzing your metagenome data

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

This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...

Free

dna-seq-gatk-variant-calling — Show Details View Workflow

This Snakemake pipeline implements the GATK best-practices workflow

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