Difference between revisions of "Count reads in transcripts (analysis)"
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:[[Institute of Systems Biology]] | :[[Institute of Systems Biology]] | ||
;Class | ;Class | ||
| − | :{{Class|biouml.plugins. | + | :{{Class|biouml.plugins.riboseq.CountReadsInTranscripts}} |
;Plugin | ;Plugin | ||
| − | :[[Biouml.plugins. | + | :[[Biouml.plugins.riboseq (plugin)|biouml.plugins.riboseq (RiboSeq Experiment)]] |
==== Description ==== | ==== Description ==== | ||
| − | For each transcript count the number mapped NGS reads from BAM file | + | For each transcript count the number mapped NGS reads from BAM file. |
==== Parameters: ==== | ==== Parameters: ==== | ||
* '''BAM track''' – BAM track with read alignments | * '''BAM track''' – BAM track with read alignments | ||
| − | * '''Ensembl''' – Ensembl database | + | * '''Transcript set''' – Transcript set |
| − | * '''Transcript subset''' – | + | ** '''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 | * '''Output table''' – Output table with read counts for each transcript | ||
[[Category:Analyses]] | [[Category:Analyses]] | ||
| − | [[Category: | + | [[Category:Ribosome profiling (analyses group)]] |
[[Category:ISB analyses]] | [[Category:ISB analyses]] | ||
[[Category:Autogenerated pages]] | [[Category:Autogenerated pages]] | ||
Latest revision as of 18:15, 9 December 2020
- Analysis title
Count reads in transcripts
- Provider
- Institute of Systems Biology
- Class
CountReadsInTranscripts- Plugin
- biouml.plugins.riboseq (RiboSeq Experiment)
[edit] Description
For each transcript count the number mapped NGS reads from BAM file.
[edit] 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
