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INTRODUCTION

This is a catalogue of diverse scripts used at the lab for smaller customised tasks.

SUPPORTED PLATFORMS AND DEPENDENCIES

Linux, Mac OS

Shell scripts (*.sh) of this software were developed and tested using GNU bash (v4.4.20) in a Ubuntu 18.04 linux system. R scripts were developed using the R console (v4.1.1) in macOS Monterey. Perl scripts tested on v5.32.1.

TOOLS

fastq_header.pl

In pair-end (PE) fastq files the sequence identifiers in line 1 (of 4) of each sequence are identical in both read1 and read2 files. Sometimes one wants to concatenate (cat) both paired-end files to a single-end (SE) fastq file for downstream analysis. This creates a fastq file were each sequence identifier is present twice, therefore not unique. This lack of uniqueness can cause bugs down the line at some processes like e.g. deduplication. This script adds endings '/1' and '/2' to the identifier of each read in the pair to make them unique prior to concatenation.

Usage:

perl fastq_header.pl sample_r1.fastq sample_r2.fastq

This creates two output files sample_r1.fastq_headed.fastq and sample_r2.fastq_headed.fastq

Looking like this in the first three fastq identifiers (header):

@A00627:342:HHL5LDSX3:3:1101:14479:1016/1
@A00627:342:HHL5LDSX3:3:1101:23032:1016/1
@A00627:342:HHL5LDSX3:3:1101:1597:1031/1

@A00627:342:HHL5LDSX3:3:1101:14479:1016/2
@A00627:342:HHL5LDSX3:3:1101:23032:1016/2
@A00627:342:HHL5LDSX3:3:1101:1597:1031/2

cytosine_conversion_calculator.pl

Evaluates nuclear and chloroplast CHH methylation to estimate cytosine non-conversion and other errors in bisulfite treated sequencing reads (BS-Seq) in Arabidopsis TAIR10. Input is the methylation report produced by the bismark_methylation_extractor (CX_report) from the BS-seq mapping tool bismark, which can look like:

Chr2	1001	-	0	0	CHH	CNN
Chr2	1006	+	0	0	CG	CGT
Chr2	1007	-	0	0	CG	CGA
Chr2	1009	+	0	0	CG	CGA
Chr2	1010	-	0	0	CG	CGA
Chr2	1012	+	0	0	CHH	CCA
Chr2	1013	+	0	0	CHG	CAG

Usage:

perl cytosine_conversion_calculator.pl sample.deduplicated.CX_report.txt

Produces standard output like:

The mean chloroplast CHH methylation is :0.663193735143279% 
The mean nuclear CHH methylation is :2.04898463286775%

CONTACT

juan.santos at slu.se