santiagosnchez/competitive_mapping_workflow

Pipeline and workflow for RNA-seq processing, differential expression and allele-specific expression analyses (and more).

Repository with workflow for competitive read mapping and allele-specific expression counts

Description of the repository

In the main directory you will find bash scripts named from 1 to 4. They should be run in that order (see Requirements).

Script 1

It will download the raw reads directly from SRA with fasterq-dump using the accession numbers stored in metadata-7938743-processed-ok.tsv and rename them. Next step is to filter and trim reads with trimmomatic.

Script 2

Generates genome indices for star based on files stored in references.

Script 3

Maps reads using star and generates BAM files as well as their indices.

Script 4

Counts reads for parent species alignments using featureCounts and for hybrid data and allele-specific expression it uses CompMap. It will also generate tables with raw counts for each sample.

Simulations

This directory includes bash and r scripts running RNA-seq data simulations for allele-specific expression using the package polyester.

Counts

All the raw count tables are included here.

Analyses

This contains two subdirectories scripts and tables.

scripts has further subdirectories with r scripts to generate summary tables from differential expression (and other) analyses. tables has all the raw summary tables used for this work.

Running some of the r scripts will overwrite the files already in that directory. So do it carefully!

Extra files

• briggsae.nigoni.1-to-1.orto.dnds_final.csv --> Includes dN, dS estimates for each ortholog
• c_briggsae_genes_conv_to_wormbase.csv --> CSV tables with equivalent gene names for the current C. briggsae WormBase release (PRJNA10731)
• orthologs.txt --> A list with C. briggsae and C. nigoni orthologs
• samples.txt --> List of sample names used for renaming files

Requirements

Unix command-line programs

• samtools
• CompMap
• GNU-parallel
• star
• BWA
• trimmomatic
• sratools
• featureCounts

R packages

• polyester
• glimma
• edgeR
• DESeq2
• MASS
• RColorBrewer
• cowplot
• dplyr
• edgeR
• ggVennDiagram
• ggforce
• ggplot2
• ggplotify
• ggpointdensity
• ggrepel
• ggridges
• ggstance
• ggtext
• grid
• gridExtra
• gtable
• lemon
• parallel
• scales
• tibble
• tidyr
• venneuler
• viridis