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BioPipelines

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.

index_reference.sh

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

mapping_pipeline.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

qc_fastq.sh

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

count_overlaps_bam_gtf.R

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.

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personal scripts for common bioinformatic pipelines

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