Micro RNA secondary analysis

[Nicklas Nordborg]

See also ticket #1606. This ticket is for the secondary analysis pipeline.

The first step is to align the data. This has originally been done with novoalign which requires a license. We need to check if and how we can do this with Singularity containers. We should investigate if other aligners could be used instead.

After alignment we have some (old) perl scripts that calculate expressions and some other things.

[Nicklas Nordborg]

In 7822:

References #1607: Micro RNA secondary analysis

Started to implement the wizard for Small RNA alignment. It is possible to selected merged sequences but it will only submit empty jobs to the cluster.

[Nicklas Nordborg]

In 7823:

References #1607: Micro RNA secondary analysis

Implemented alignment with sRNAMapper (​https://github.com/mzytnicki/srnaMapper). We may change to Novoalign later if that produces better results. Some statistics is also needed but it has not been implemented yet.

[Nicklas Nordborg]

In 7824:

References #1607: Micro RNA secondary analysis

Added samtools flagstat to the script. The "primary mapped" value is parsed out and stored in the new ALIGNED_READS annotation.

[Nicklas Nordborg]

In 7825:

References #1607: Micro RNA secondary analysis

Added a "sRNA" section to the case summary.

[Nicklas Nordborg]

In 7826:

References #1607: Micro RNA secondary analysis

Implemented manual and automatic confirmation of alignment.