From 29ab8d946666b76a75af5b440944061e705e7ad5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?St=C3=A9phanie=20Robin?= Date: Thu, 30 May 2024 17:52:49 +0200 Subject: [PATCH] updating tutorial with new bam file --- .../tutorials/lncrna/data-library.yaml | 14 +++++++------- .../tutorials/lncrna/tutorial.md | 16 ++++++++-------- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/topics/genome-annotation/tutorials/lncrna/data-library.yaml b/topics/genome-annotation/tutorials/lncrna/data-library.yaml index 203a3f48e8a6ac..4372bd86b398ee 100644 --- a/topics/genome-annotation/tutorials/lncrna/data-library.yaml +++ b/topics/genome-annotation/tutorials/lncrna/data-library.yaml @@ -10,18 +10,18 @@ items: items: - name: Long non-coding RNAs (lncRNAs) annotation with FEELnc items: - - name: 'DOI: 10.5281/zenodo.7107050' + - name: 'DOI: 10.5281/zenodo.11367439' description: latest items: - - url: https://zenodo.org/api/files/0f8d27c5-8c8d-4379-90c4-c3cd950de391/genome_assembly.fasta + - url: https://zenodo.org/api/records/11367439/files/genome_assembly.fasta/content src: url ext: fasta - info: https://zenodo.org/record/7107050 - - url: https://zenodo.org/api/files/0f8d27c5-8c8d-4379-90c4-c3cd950de391/genome_annotation.gff3 + info: https://zenodo.org/record/11367439 + - url: https://zenodo.org/api/records/11367439/files/genome_annotation.gff3/content src: url ext: gff3 - info: https://zenodo.org/record/7107050 - - url: https://zenodo.org/api/files/0f8d27c5-8c8d-4379-90c4-c3cd950de391/all_RNA_mapped.bam + info: https://zenodo.org/record/11367439 + - url: https://zenodo.org/api/records/11367439/files/SRR8534859_RNASeq_mapped.bam/content src: url ext: bam - info: https://zenodo.org/record/7107050 + info: https://zenodo.org/record/11367439 diff --git a/topics/genome-annotation/tutorials/lncrna/tutorial.md b/topics/genome-annotation/tutorials/lncrna/tutorial.md index 18ab930c15db13..e18e1672b6f7c9 100644 --- a/topics/genome-annotation/tutorials/lncrna/tutorial.md +++ b/topics/genome-annotation/tutorials/lncrna/tutorial.md @@ -2,7 +2,7 @@ layout: tutorial_hands_on title: Long non-coding RNAs (lncRNAs) annotation with FEELnc -zenodo_link: https://zenodo.org/record/7107050 +zenodo_link: https://zenodo.org/records/11367439 tags: - eukaryote questions: @@ -89,9 +89,9 @@ To assemble transcriptome with StringTie and annotate {lncRNAs} with FEELnc, we > -> `{{ page.title }}`): > > ``` -> https://zenodo.org/record/7107050/files/genome_assembly.fasta -> https://zenodo.org/record/7107050/files/genome_annotation.gff3 -> https://zenodo.org/record/7107050/files/all_RNA_mapped.bam +> https://zenodo.org/records/11367439/files/genome_assembly.fasta +> https://zenodo.org/records/11367439/files/genome_annotation.gff3 +> https://zenodo.org/records/11367439/files/SRR8534859_RNASeq_mapped.bam > ``` > > {% snippet faqs/galaxy/datasets_import_via_link.md %} @@ -111,7 +111,7 @@ A reference annotation file in GTF or GFF3 format can be provided to StringTie w > > {% tool [StringTie](toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.7+galaxy1) %} with the following parameters: > - *"Input options"*: `Short reads` -> - {% icon param-file %} *"Input short mapped reads"*: `all_RNA_mapped.bam` +> - {% icon param-file %} *"Input short mapped reads"*: `SRR8534859_RNASeq_mapped.bam` > - *"Specify strand information"*: Unstranded > - *"Use a reference file to guide assembly?"*: Use reference GTF/GFF3 > - *"Reference file"*: Use a file from history @@ -172,11 +172,11 @@ FEELnc provides also summary file in stdout. > > > > > -> > The summary file indicates 104 {lncRNAs} and 0 new {mRNAs} were annotated by FEELnc. The initial annotation contains 13,795 {mRNAs} annotated. Therefore, a total of 13,898 RNAs are currently annotated. +> > The summary file indicates 268 {lncRNAs} and 0 new {mRNAs} were annotated by FEELnc. The initial annotation contains 13,795 {mRNAs} annotated. Therefore, a total of 14,063 RNAs are currently annotated. > > -> > The summary file indicates 652 interactions between {lncRNAs} and {mRNAs}. These interactions are described in the Classifier output file. +> > The summary file indicates 772 interactions between {lncRNAs} and {mRNAs}. These interactions are described in the Classifier output file. > > -> > The different types of {lncRNAs} (intergenic (sense and antisense), intragenic (sense)) are described in the Classifier output file. We observe that the majority of the {lncRNAs} are intergenic. These {lncRNAs} can each have interactions with several {mRNAs}. Only 7 {lncRNAs} are genic. These {lncRNAs} have only one interaction with the mRNA that contains it. +> > The different types of {lncRNAs} (intergenic (sense and antisense), intragenic (sense)) are described in the Classifier output file. We observe that the majority of the {lncRNAs} are intergenic. These {lncRNAs} can each have interactions with several {mRNAs}. Only 5 {lncRNAs} are genic. These {lncRNAs} have only one interaction with the mRNA that contains it. > > > {: .solution} >