miscellaneous tools for analysis of RNA-seq data
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prep
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LICENSE.md
README.md
extract_fasta_from_gff.rb
prep_and_trim.sh
trim-batch.rb

README.md

RNASeq tools

A collection of tools for analysis of RNA-seq and transcriptomic data used by the Hibberd Lab.

Batch read processing scripts

  • trim-batch - run trimmomatic on a series of FASTQ read files, optionally trimming paired and single reads in the same run. After quality analysis, this is the first step in an RNASeq pipeline.
  • khmer-batch - run digital normalisation on a series of FASTQ read files, preserving the kmer counting hash between runs, to create a single normalised read dataset. Useful for incorporating a new read dataset with old data to generate an improved de-novo assembly.

License

All files released under the permissive MIT 'Expat' license unless otherwise specified.

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