Module: bbcflib.rnaseq

Methods of the bbcflib’s RNA-seq worflow. The main function is rnaseq_workflow().

From a BAM file produced by an alignement on the genome, gets counts of reads on the exons, and uses least-squares to infer counts on genes and transcripts.

class bbcflib.rnaseq.RNAseq(ex, via, job, assembly, conditions, debugfile, logfile, pileup_level, junctions, stranded)[source]

Bases: object

Abstract, inherited by different parts of the workflow.

bbcflib.rnaseq.gtf_from_bam_header(bam)[source]

In case of alignment on a custom sequence.

bbcflib.rnaseq.transcriptome_gtf_from_genrep(assembly)[source]

In case of mapping on the transcriptome - it if still ever happens.

bbcflib.rnaseq.rnaseq_workflow(*args, **kwargs)[source]

Main function of the workflow.

Return type:

None

Parameters:
  • ex – a bein execution.
  • job – a Frontend.Job object (or a dictionary of the same form).
  • assembly – a genrep.Assembly object
  • junctions – (bool) whether to search for splice junctions using SOAPsplice. [False]
  • via – (str) send job via ‘local’ or ‘lsf’. [“lsf”]

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