This repository hosts scripts and tools for analysis of high throughput sequencing data.
Made for SLURM & Environment Modules Project
This is the script we use for downloading genome assemblies from ENSEMBL and build the respective indexes and folders structure.
For usage check the help output:
./ensref --help
The former script ENSrefs is deprecated. See the history with
git log -- ENSrefs build-ref.sh
git log -p -- ENSrefs build-ref.sh # with diff
this script takes a wget command from CCG donwload instructions, downloads the respective files to a destination of choice checking file integrity afterwards.
usage:
CCG -l "wget ..." -o destination_folder
This script allows you to generate a fasta file for a chromosome contained in a multifasta file.
Usage:
getChromosome -h
# For >2 dna:chromosome chromosome:GRCm38:2:1:182113224:1 REF use:
getChromosome -i GRCm38.dna.primary_assembly.fa -o output_folder -c 2
Create genome file for bedtools. The output is a tab-delimited file of chromosome name followed by its length.
Usage:
make.genome -h
This scripts lifts fasta files from GATK reconstructions (ie. FastaAlternateReferenceMaker).
Usage:
GATKlift -h
Made for SLURM & Environment Modules Project
This script runs a full RNAseq pipeline under a slurm jobs distribution system
- fastQC - quality control
- flexbar - adapters and quality trimming
- tophat - aligner
- cufflinks - transcripts assembly and quantification
- cuffmerge - merging of assemblies
- cuffcompare - corrrection of lost protein ids
- cuffquant - transcript expression profiles
- cuffdiff - differential expression analysis
Please read the instructions inside the script for usage.
Made for SLURM & Environment Modules Project
This script runs a full RNAseq pipeline under a slurm jobs distribution system using about 18 processes per file allowing full analysis of 20 libraries with 50 - 150 M reads per library to complete under 12h
- fastQC - quality control
- flexbar - adapters and quality trimming
- hisat - aligner
- stringtie - transcripts assembly and quantification
- cuffmerge - merging of assemblies
- cuffquant - transcript expression profiles
- cuffdiff - differential expression analysis
Please read the instructions inside the script for usage.
This python script takes cuffdiff results as inputs and generates excel report tables for each parallel comparison. It annotates each gene with the respective GO and KEGG term. It also uses DAVID to perform GO enrichment analysis of biological process, cellular components, molecular function and other DAVID annotations using significantly changed genes, transcripts, promoter usage, splicing, CDS.
Usage:
aDiff -h
A command line tool to annotate ids in a column of tables (.tsv, .csv, .xls[x] format) with the R/biomaRt tool and optionally merge the result with the original table.
Dependencies:
- python >= 2.7
- python/argparse
- R (tested on version 3.2)
- R/WriteXLS
- R/argparse
- R/biomaRt
- R/plyr
- R/readxl
Usage:
mart -h
This R script performs a minimal quality control analysis on cuffdiff outputs. The output folder needs to be created before using this script. Not all plot allways perform with every dataset - you might therefore need to comment out some plots.
This R scripts requires the cummeRbund package. To install it, run the following
in an R console:
source('http://www.bioconductor.org/biocLite.R')
biocLite('cummeRbund', ask=FALSE)
Usage:
mkdir cummeRbund_output_folder
Rscript QC.R cuffdiff_output_folder cummeRbund_output_folder
This executable interactive python scripts lets you merge `*.tabular files outputed by CloudMap and filter SNPs of interest based on the maximum number of samples containing the SNP and minimum number of SNPs per gene.
Usage:
SNPsFilter
A HPC/slurm pipeline to perform RNA methylation analysis. Modify the sample sheet and path variables at the beginning of the script. Run script on trimmed read data. Submit in slurm environment.
Made for SLURM & Environment Modules Project
This is a standard GATK and lofreq variant call pipeline with snpEff annotations. It is made to make calls on two lines eg. wt and mutant. It is set for single end sequencing. Please read the instructions inside the script for usage.
Made for SLURM & Environment Modules Project
This template lets you create chain files for 2 fasta files of the same species after genome reconstruction or de-novo assembly.
This script should be run from project/scripts/chains_slurm.sh
More info can be found here: http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/doc/liftOver.txt and here: http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver
Usage:
./chains_slurm.sh /path/to/old/fasta.fa /path/to/new/fasta.fa
The respective chains file can be found in chains_output/oldFasta_To_newFasta.chain.gz
Working Python implementation of CellPlot and SymPlot from the CellPlot package for R.
usage: CellPlot [-h] [-i INPUT] [-n NTERMS] [-o OUTPUT]
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Tab separated tables with the following collumns from
an enrichment analysis: 'Enrichment', 'Significant',
'Annotated', 'Term', and 'log2fc'. For log2fc each
cell must contain a comma separated string with the
log2fc for the genes enriched in the respective term.
eg. '-Inf,-1,2,3.4,3.66,Inf' (default: None)
-n NTERMS, --nterms NTERMS
Number of terms to display (default: 10)
-o OUTPUT, --output OUTPUT
/path/to/output/prefix This will create the files
prefix.CellPlot.svg, prefix.CellPlot.png,
prefix.SymPlot.svg, prefix.SymPlot.png (default: None)
Run gene ontology enrichment analysis using R/Bioconductor's topGO package.
Usage:
usage: topgo [-h] [-i NAME] [-e NAME] [-n NAME [NAME ...]] [-f FORMAT]
[-o OUTPUT_PREFIX] [-x] [-v] [-w]
organism table [table ...]
topgo - perform gene ontology enrichment analysis using Bioconductor/topGO
positional arguments:
organism Select organism [second field as identifier from
Bioconductor AnnotationDbi 'org' databases]. E.g. 'Dm'
for 'org.Dm.eg.db'. Supported are Ag = Anopheles, Bt =
Bovine, Ce = Worm, Cf = Canine, Dm = Fly, Dr =
Zebrafish, Gg = Chicken, Hs = Human, Mm = Mouse, Mmu =
Rhesus, Pt = Chimp, Rn = Rat. See also: http://biocond
uctor.org/packages/release/BiocViews.html#___OrgDb
Currently unsupported are At, EcK12, EcSakai, Pf, Ss,
Xl.
table Path to tabular input file(s).
optional arguments:
-h, --help show this help message and exit
-i NAME, --id-column NAME
Column name of gene identifiers (Ensembl gene ids) to
query. (default: gene)
-e NAME, --expression-column NAME
Column name of gene expression values. Merged into
output column 'GenesSignificantExpression'. (default:
None)
-n NAME [NAME ...], --name-columns NAME [NAME ...]
Column name(s) for other values to be coerced as
lists. Merged into output column
'GenesSignificantNAME'. (default: None)
-f FORMAT, --input-format FORMAT
Select the input file format. (default: tsv)
-o OUTPUT_PREFIX, --output-prefix OUTPUT_PREFIX
Output file prefix. Can contain slashes for (sub)
folders. Prepended to input file base names without
suffix and sheet names. (default: topgo.)
-x Also output a .xlsx version. (default: False)
-v, --verbose Be more verbose on what is done. (default: False)
-w, --show-warnings Show 'warnings()' after reading tables. (default:
False)
Create plots from gene ontology or other enrichment analysis.
Usage:
usage: goplots [-h] [-s SHEETS] [-d DELIMITER] [--col-term COL_TERM]
[--col-enrich COL_ENRICH] [--col-nsign COL_NSIGN]
[--col-nannotated COL_NANNOTATED] [--col-deg COL_DEG] [-f]
[-n NTERMS] [-o OUTPUT_FOLDER]
table [table ...]
positional arguments:
table Input table
optional arguments:
-h, --help show this help message and exit
-s SHEETS, --sheets SHEETS
Sheet for xl input (default: None)
-d DELIMITER, --delimiter DELIMITER
For text input files, the column separator (default: )
--col-term COL_TERM Column name for term names/ids (default: termName)
--col-enrich COL_ENRICH
Column name for (log) fold enrichment values (default:
foldEnrichment)
--col-nsign COL_NSIGN
Column name for number of significant genes (default:
listHits)
--col-nannotated COL_NANNOTATED
Column name for number of annotated genes (default:
Annotated)
--col-deg COL_DEG Column name for differential gene expression (e.g.
logFC-) values (default: geneExpression)
-f, --format-deg Replace missing gene expression values by mean of
values per term (default: False)
-n NTERMS, --nterms NTERMS
Number of terms to plot (default: 20)
-o OUTPUT_FOLDER, --output-folder OUTPUT_FOLDER
Output directory (default: goplots_output)
Create cellplot and symplot plots from david output.
Usage:
./david_to_cellplot.R [infile] [fileype] [category] [nterms]
- filetype:
xlsxtsvcsvtxt - category: anything present in the DAVID output file
- nterms: number of terms to plot
Copyright 2016, Bioinformatics Core Facility of the Max Planck Institute for Biology of Ageing
See file LICENSE.