Simple pipeline for processing of sequencing data from thCHART, ChIP-seq, APEX-ChIP and similar experiments
This is a script to process .fastq sequencing files from thCHART, CHART or ChIP-seq experiments and genereate fold-enrichment tracks in bigWig format.
Script must be started from folder with all .fastq files. Sample names must match filename format: NAME_R1.fastq NAME_R2.fastq
Usage: chart-analyze.sh -g [genome version] -r [read type] [-u] -i [input[,input2]] -s [sample1[,sample2...]]
e.g. chart-analyze.sh -g dm6 -r PE -i MM200201_01 -s MM200201_02,MM200201_03,MM200201_04
parameters: -s|--samples - comma-separated list of sample name(s)
-i|--input - input sample name
-g|--genome - name of genome to use [dm6, dm3, hg38, hg19, hg18, mm9, mm10]
-r|--reads - type of reads [PE, SE]
-u|--uniqalign - keep only uniquely aligned reads by applying mapping quality filter in samtools -q 2
-h|--help - this message