View source for Count reads in transcripts (analysis)

;Analysis title
:[[File:Default-analysis-icon.png]] Count reads in transcripts
;Provider
:[[Institute of Systems Biology]]
;Class
:{{Class|biouml.plugins.riboseq.CountReadsInTranscripts}}
;Plugin
:[[Biouml.plugins.riboseq (plugin)|biouml.plugins.riboseq (RiboSeq Experiment)]]

==== Description ====
For each transcript count the number mapped NGS reads from BAM file.

==== Parameters: ====

* '''BAM track''' – BAM track with read alignments
* '''Transcript set''' – Transcript set
** '''Annotation source''' – Source of gene annotation
** '''Transcripts annotation track''' – Track with transcripts annotation in BED format
** '''Genome sequence''' – Collection of chromosomal sequences
** '''Ensembl''' – Ensembl database version
** '''Transcript subset''' – Subset of transcripts used in this analysis
** '''GTF file''' – GTF file
* '''Strand specific''' – Count only reads on the same strand as transcript
* '''Only overlapping cds''' – Count only reads that overlap coding sequence
* '''Min overlap''' – Minimal overlap between read and CDS in nucleotides
* '''Output table''' – Output table with read counts for each transcript

[[Category:Analyses]]
[[Category:Ribosome profiling (analyses group)]]
[[Category:ISB analyses]]
[[Category:Autogenerated pages]]