Personal scripts to run general and often-used pipelines. In all cases, it might be necessary to adjust variables with paths to GATK and Picard Tools.
Indexes a reference genome with bowtie2-build, samtools faidx,
CreateSequenceDictionary from Picard Tools and bwa index.
Instructions of usage can be obtained by running the script with no
options: bash index_reference.sh
Does mapping and post-mapping steps using several tools, including indel-realignment.
Instructions of usage can be obtained by:
bash mapping_pipeline.sh -h
Quality control and filtering using FastQC and cutadapt. Uses GNU parallel to parallelize filtering of the reads.
Instructions of usage can be obtained by:
bash qc_fastq.sh -h
An R script to count read alignments overlapping an annotation (GTF) file.
Instructions for usage can be obtained by:
Rscript count_overlaps_bam_gtf.R --help
The script depends on the following packages:
The pipeline is based on this BioConductor tutorial.