Difference between revisions of "ComputeTranscriptProfile (analysis)"
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* '''BAM files''' – BAM files with genomic alignments | * '''BAM files''' – BAM files with genomic alignments | ||
| − | * '''Annotation source''' – Source of gene annotation | + | * '''Transcript set''' – Transcript set |
| − | * '''Transcripts annotation track''' – Track with transcripts annotation in BED format | + | ** '''Annotation source''' – Source of gene annotation |
| − | * '''Ensembl''' – Ensembl database version | + | ** '''Transcripts annotation track''' – Track with transcripts annotation in BED format |
| − | * '''Transcript subset''' – Subset of transcripts used in this analysis | + | ** '''Genome sequence''' – Collection of chromosomal sequences |
| + | ** '''Ensembl''' – Ensembl database version | ||
| + | ** '''Transcript subset''' – Subset of transcripts used in this analysis | ||
| + | ** '''GTF file''' – GTF file | ||
* '''Transcript overhangs''' – Transcript overhangs | * '''Transcript overhangs''' – Transcript overhangs | ||
* '''Strand specific''' – In strand specific protocol reads can come only from positive strand of transcript | * '''Strand specific''' – In strand specific protocol reads can come only from positive strand of transcript | ||
* '''Ribosome A-site offset table''' – Table with 2 columns: <nowiki>'</nowiki>Length<nowiki>'</nowiki> and <nowiki>'</nowiki>Offset<nowiki>'</nowiki> | * '''Ribosome A-site offset table''' – Table with 2 columns: <nowiki>'</nowiki>Length<nowiki>'</nowiki> and <nowiki>'</nowiki>Offset<nowiki>'</nowiki> | ||
* '''Min transcript footprints''' – Minimal number of footprints in transcript | * '''Min transcript footprints''' – Minimal number of footprints in transcript | ||
| + | * '''Processed transcript''' – Compute profile for processed transcript (without introns) | ||
* '''Output track''' – Resulting track with transcript profiles | * '''Output track''' – Resulting track with transcript profiles | ||
Revision as of 19:01, 13 February 2017
- Analysis title
ComputeTranscriptProfile
- Provider
- Institute of Systems Biology
- Class
ComputeTranscriptProfile- Plugin
- biouml.plugins.riboseq (RiboSeq Experiment)
Description
Compute footprint profile for transcripts
Parameters:
- BAM files – BAM files with genomic 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
- Transcript overhangs – Transcript overhangs
- Strand specific – In strand specific protocol reads can come only from positive strand of transcript
- Ribosome A-site offset table – Table with 2 columns: 'Length' and 'Offset'
- Min transcript footprints – Minimal number of footprints in transcript
- Processed transcript – Compute profile for processed transcript (without introns)
- Output track – Resulting track with transcript profiles
