From abfbbb4237caff0787d5ee9b2595cb470b1af954 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Fri, 13 Dec 2024 16:40:39 +0100 Subject: [PATCH] update more hands-on paramters --- .../ENA_Biodiv_submission/tutorial.md | 64 +++++++++++-------- 1 file changed, 37 insertions(+), 27 deletions(-) diff --git a/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.md b/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.md index ab434424628a16..baa7c2b7601030 100644 --- a/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.md +++ b/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.md @@ -47,6 +47,7 @@ The goal is to present an accessible and reproductible workflow for data submiss # Prepare raw data > Data Upload +> > 1. **Create a new history** for this tutorial > > {% snippet faqs/galaxy/histories_create_new.md %} @@ -58,8 +59,6 @@ The goal is to present an accessible and reproductible workflow for data submiss > https://data.indores.fr/api/access/datafile/3609 > ``` > -> -> > {% snippet faqs/galaxy/datasets_import_via_link.md %} > > 3. **Rename** {% icon galaxy-pencil %} your datafiles @@ -87,8 +86,9 @@ Following steps take as input ab1 sequences files and produce filtered FastQ and ### Converting Ab1 files to FASTQ > ab1 to FASTQ converter +> > 1. {% tool [ab1 to FASTQ converter](toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0) %} with the following parameters: -> - {% icon param-file %} *"Input ab1 file"*: `ab1` data collection created at the previous step +> - {% icon param-collection %} *"Input ab1 file"*: `ab1` data collection created at the previous step > {: .hands_on} @@ -100,7 +100,8 @@ We are doing a first Quality control on the raw files using FastQC and MultiQC. > FastQC > 1. {% tool [FastQC](toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0) %} with the following parameters: > - {% icon param-file %} *"Raw read data from your current history"*: `ab1.fastq` data collection created at the previous step -> 2. {% tool [MultiQC](toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1) %} with the following parameters: +> +> 2. {% tool [MultiQC](toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1) %} with the following parameters: > - In *"Results"*: > - {% icon param-repeat %} *"Insert Results"* > - *"Which tool was used generate logs?"*: `FastQC` @@ -129,12 +130,13 @@ We are doing a first Quality control on the raw files using FastQC and MultiQC. # Cleaning the Data ## Cutadapt + Cutadapt enables the removal of adapters, polyA tails, and other artifacts from sequences. The tool also filters reads based on quality. > Cutadapt > > 1. {% tool [Cutadapt](toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0) %} with the following parameters: -> +> - {% icon param-collection %} *"FASTQ/A file"*: the collection with your data (output of {% icon tool %} **ab1 to FastQ converter**) > - **"Single-end or Paired-end reads?"**: `Single-end` > - In **"Other Read Trimming Options"**: > - **"Quality cutoff(s) (R1)"**: `30` @@ -147,23 +149,24 @@ Cutadapt enables the removal of adapters, polyA tails, and other artifacts from > {: .hands_on} -> > Quality Control -> > -> > We do a second quality control similar to the first one to check the quality of the sequences after cleaning them. -> {: .comment} +> Quality Control +> +> We do a second quality control similar to the first one to check the quality of the sequences after cleaning them. +{: .comment} + ## Quality Control with FastQC and MultiQC > FastQC > -> 1. {% tool [FastQC](toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0) %} on the cutadapt output files> -> +> 1. {% tool [FastQC](toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0) %} with the following parameters: +> - {% icon param-collection %} *"Raw read data from your current history"*: output from {% icon tool%} **Cutadapt** > > 2. {% tool [MultiQC](toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1) %} with the following parameters: > - In *"Results"*: -> - {% icon param-repeat %} *"Insert Results"* -> - *"Which tool was used generate logs?"*: `FastQC` -> +> - *"Which tool was used generate logs?"*: `FastQC` +> - {% icon param-repeat %} *"Insert FastQC output"* +> - {% icon param-collection %} *"FastQC output"*: the `raw` output from {% icon tool %} **FastQC** > > > Comment > > @@ -174,16 +177,19 @@ Cutadapt enables the removal of adapters, polyA tails, and other artifacts from ## Filtering the collection + > Filter empty datasets > -> 1. {% tool [Filter empty datasets](__FILTER_EMPTY_DATASETS__) %} on the Cutadapt resulting data collection -> +> 1. {% tool [Filter empty datasets](__FILTER_EMPTY_DATASETS__) %} with the following parameters +> - {% icon param-collection %} *"Input Collection"*: output collection from Cutadapt step > -> 2. {% tool [FASTQ Groomer](toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5+galaxy2) %} on the Filtered data collection, using default parameters. +> 2. {% tool [FASTQ Groomer](toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5+galaxy2) %} with the following parameters: +> - {% icon param-collection %} *"File to groom"* : output collection from the {% icon tool %} **Filter empty datasets** > -> This step is notably there to produce "standardized" fastqsanger sequences files si we can then use other tools accepting only such data format. +> This step is notably there to produce "standardized" fastqsanger sequences files so we can then use other tools accepting only such data format. > > 3. {% tool [Filter FASTQ](toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5) %} with the following parameters: +> - *"FASTQ File"*: output collecton from {% icon tool %} **FastQ Groomer** > - *"Minimum size"*: `300` > > > Comment @@ -193,13 +199,16 @@ Cutadapt enables the removal of adapters, polyA tails, and other artifacts from > {: .hands_on} + ### Changing files names > Extract element identifiers and remove extensions > > 1. {% tool [Extract element identifiers](toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2) %} +> - {% icon param-collection %} *"Dataset collection"*: output from the previous step > > 2. {% tool [Regex Find And Replace](toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3) %} with the following parameters: +> - *"Select lines from"*: output of the previous step > - In *"Check"*: > - {% icon param-repeat %} *"Insert Check"* > - *"Find Regex"*: `.ab1` @@ -210,13 +219,10 @@ Cutadapt enables the removal of adapters, polyA tails, and other artifacts from > > This is to ensure that all your files names end with .fastq.gz > {: .comment} > -> 3. {% tool [Paste](Paste1) %} -> - In *"Paste"*: -> - Select the file from {% tool [Extract element identifiers](toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2) %} -> - In *"and"*: -> - Select the file from {% tool [Regex Find And Replace](toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3) %} -> - *"Delimited by"*: -> - Tab +> 3. {% tool [Paste](Paste1) %} with the following parameters: +> - {% icon param-file %} *"Paste"*: the file from {% icon tool %} **Extract element identifiers** +> - {% icon param-file %} *"and"*: the file from {% icon tool %} **Regex Find And Replace** +> - {% icon param-select %} *"Delimited by"*: Tab > > 4. **Check the datatype** > - should be 'tabular'. If not, change it now. @@ -230,18 +236,21 @@ Cutadapt enables the removal of adapters, polyA tails, and other artifacts from > Relabel identifiers > > 1. {% tool [Relabel identifiers](__RELABEL_FROM_FILE__) %} with the following parameters: -> - *"How should the new labels be specified?"*: `Map original identifiers to new ones using a two column table.` +> - {% icon param-collection %} *"Input Collection"*: output from {% icon tool %} **Filter FastQ** +> - *"How should the new labels be specified?"*: `Map original identifiers to new ones using a two column table.` > {: .hands_on} -## Alignments on NCBI database +## Alignments on NCBI database > NCBI BLAST alignment > > 1. {% tool [FASTQ to FASTA](toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5) %} with the following parameters: +> - {% icon param-collection %} *"Input FASTQ File"*: output collection from {% icon tool %} **Relabel Identifiers** > > 2. {% tool [NCBI BLAST+ blastn](toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2) %} with the following parameters: +> - {% icon param-collection %} Nucleotide query sequence(s): output from the previous step > - *"Subject database/sequences"*: `Locally installed BLAST database` > - *"Nucleotide BLAST database"*: `NCBI NT (01 Sep 2023)` > - *"Output format"*: `Tabular (extended 25 columns)` @@ -252,6 +261,7 @@ Cutadapt enables the removal of adapters, polyA tails, and other artifacts from > Extracting best hits > > 1. {% tool [Unique](toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3) %} with the following parameters: +> - {% icon param-collection %} *"File to scan for unique values"*: output from the previous step > - *"Advanced Options"*: `Show Advanced Options` > - *"Column start"*: `c1` > - *"Column end"*: `c1`