Difference between revisions of "Count reads in transcripts (analysis)"

Revision as of 18:59, 13 February 2017

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

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

@@ Line 4: / Line 4: @@
 :[[Institute of Systems Biology]]
 ;Class
-:{{Class|biouml.plugins.ensembl.analysis.CountReadsInTranscripts}}
+:{{Class|biouml.plugins.riboseq.CountReadsInTranscripts}}
 ;Plugin
-:[[Biouml.plugins.ensembl (plugin)|biouml.plugins.ensembl (Support for Ensembl database and Ensembl-specific analyses)]]
+:[[Biouml.plugins.riboseq (plugin)|biouml.plugins.riboseq (RiboSeq Experiment)]]
 ==== Description ====
@@ Line 14: / Line 14: @@
 * '''BAM track''' – BAM track with read alignments
-* '''Ensembl''' – Ensembl database
+* '''Transcript set''' – Transcript set
-* '''Transcript subset''' – Calculate read count only for these transcripts
+** '''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