Difference between revisions of "Estimate read density (analysis)"
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==== Description ==== | ==== Description ==== | ||
| − | Estimate read density in transcripts and CDS using mappability information | + | Estimate read density in transcripts and CDS using mappability information. |
==== Parameters: ==== | ==== Parameters: ==== | ||
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Latest revision as of 18:15, 9 December 2020
- Analysis title
Estimate read density
- Provider
- Institute of Systems Biology
- Class
EstimateReadDensity- Plugin
- biouml.plugins.riboseq (RiboSeq Experiment)
[edit] Description
Estimate read density in transcripts and CDS using mappability information.
[edit] Parameters:
- Alignments – Genomic alignments of reads to transcriptome
- Minimal unique length – Minimal unique length file, produced by 'Transcriptome minimal unique length' analysis
- 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 mapped to forward strand of transcript
- In CDS – Compute density in CDS
- Min CDS overlap – Include only reads overlapping this number of nucleotides with CDS
- Output density table – Output density table
