Basic script for differential gene expression analysis with DESeq2
Takes a directory of bam files and for each file counts reads mapping to regions in a specified bed file. If a total_mapped_reads.txt file exists, this can be used to calculate normalized read counts
Dependency for bed_count.sh
Used to collapse identical reads (often used in sRNA data to counteract the effect of "jackpotting"). Contains an option to uncollapsed a collapsed file.
Run fastqc on a directory of samples
Get GO terms from DESeq2 output file.
Makes bedgraph file showing coverage for a group of bam files at specified loci
Makes normalized BigWig files from a directory of bam files. Tracks are normalized to the mean total mapped reads per library.
Merges read count files made from individual bam files into a single file that can be loaded straight into DESeq
Contains some basic processing steps for RNA-seq data that don't involve DESeq (eg. normalizing to total mapped reads)
Run the picard duplicate removal utility on a batch of bam files
Converts between fasta/fastq/raw file types. Optionally filters for reads based on sequence features (eg. 22 nucleotides long, beginning with a "G") and allows for 3' trimming (eg. to get rid of A-tails).
Download SRR files from sample IDs (eg. GSM IDs from GEO) and extract fastq files
Basic script for trimming reads with bbduk