Try adding circall

[kopardev]

Circall should be easy to implement as docker is available at docker://ndatth/circall:v1.0.1 Steps:

• pull docker as singularity
• create sqlite db with createSqlite.R
• build BSJ fasta with buildBSJdb.R
• use gffread from cufflinks to create transcript fasta
• create Transcriptome and BSJ indexes with TxIndexer from the fastas
• run Circall.sh to call circRNAs

[kopardev]

Observations:

• too much custom-prep required to run
• run completed but has error Error: object 'PEres' not found Execution halted
• Too few circRNAs called ~60 instead of ~3000
• too dependent on existing exon annotations ... probably unfit for novel circRNA calls
• all circRNAs are human ... no virus circRNAs detected VERDICT : DO NOT ADD