small-rna-seq-pipeline - Release v0.4.4

This release fix a bug with the unique cluster identifier assignment. When concatenating all individual shortstack files, it is essential to assign a unique identifier to all identified sRNA clusters.

- Python
Published by mgalland over 5 years ago

small-rna-seq-pipeline - Release v0.4.3

With Blast version 2.9

- Python
Published by mgalland about 6 years ago

small-rna-seq-pipeline - Release 0.4.2

Add a small script to generate a small RNA library for testing purposes.

- Python
Published by mgalland about 6 years ago

small-rna-seq-pipeline - Release 0.4.0

New functionalities added:

• Now outputs a concatenated Shortstack file called "concatenatedshortstacks.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 "clusterunique_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).

- Python
Published by mgalland over 6 years ago

small-rna-seq-pipeline - Version 0.2.0

Release with plots version.

- Python
Published by mgalland over 6 years ago