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Release 0.4.0

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@mgalland mgalland released this 23 Mar 17:25
· 42 commits to master since this release
v0.4.0
508ca27

New functionalities added:

  • Now outputs a concatenated Shortstack file called "concatenated_shortstacks.tsv" that contains all predicted sRNA loci from all samples. Small RNA loci corresponding to a MIR gene hairpin will have the hairpin sequence added. Finally, a unique cluster id (column "cluster_unique_id") is added so that all individual sRNA loci from every sample will have a unique identifier. That can be useful when several sRNA loci correspond have a common MIR gene homolog in miRBase for instance.

  • Uses a "samples.tsv" file to list the sample names, their fastq file location and the genomic reference to use.

  • Calculate the minimal folding energy for all predicted hairpins using Vienna RNA RNAfold program. This information can be used to fold the stem-loop structure of hairpins (using the RNAplot program from Vienna RNA package).

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