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Spencer Mahaffey edited this page Feb 8, 2018
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Most scripts assume the following directory structure
/.../batch/
rawReads
trimmedReads
v1
cleanedReads
rn6.v1
alignedReads
rn6.v1
- Trimming - Trim reads for quality and adapter sequence (optionally count raw reads) - cutadapt
- Cleaning - Align to rRNA to remove rRNA - bowtie2
- Genome Alignment - Align either trimmed or cleaned reads to genome using either strain specific genomes or a generic reference - hisat2
- RSEM - Align and quantitate a transcriptome - RSEM
- Small RNA Alignmet - a series of steps to align to strain specific smallRNA features seperated into miRNA, snoRNA, miscSmallRNA, miscLargeRNA and aligned in that order by aligning unaligned reads from the preceeding step - bowtie2
- Stranded bamToBigWig - convert bam files to stranded bigWig files
- zip files - zip a folder of files with a specific suffix, runs N files in parallel.
- bamToFastQ - bamToFastQ conversion while removing unpaired reads - called during the cleaning step to generate unmapped.end1/2.fq.gz files for use in the remainder of the pipeline/tools.
- count zipped fastq - script to automatically count lines in all zipped fastq within a folder - leaving all the files zipped.