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Update tutorial.md first pass
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yvanlebras authored Dec 16, 2023
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Showing 1 changed file with 4 additions and 4 deletions.
8 changes: 4 additions & 4 deletions topics/ecology/tutorials/Manage_AB1_Sanger/tutorial.md
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Expand Up @@ -174,7 +174,7 @@ This following hands-on is to be applied only on the sequence of the antisense (
> > How many files is there in the ZIP archive ?
> >
> > > ### {% icon solution %} Solution
> > > 12 (if you have a different number of files something likely went srong)
> > > 12 (if you have a different number of files something likely went wrong)
> > >
> > {: .solution}
> >
Expand All @@ -193,7 +193,7 @@ As for primers, sense and antisense sequences will be subjected to slightly diff
> <hands-on-title> Filter </hands-on-title>
>
> 1. {% tool [Extract element identifiers](toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2) %} with the following parameters:
> - {% icon param-collection %} *"Dataset collection*: `output collection` (output of **Unzip** {% icon tool %})
> - {% icon param-collection %} *"Dataset collection"*: `output collection` (output of **Unzip** {% icon tool %})
>
> 2. {% tool [Regex Find And Replace](toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3) %} with the following parameters:
> - {% icon param-file %} *"Select lines from"*: `output` (output of **Extract element identifiers** {% icon tool %})
Expand Down Expand Up @@ -332,7 +332,7 @@ See in the introduction for explanations on the Reverse-Complement.
> >
> {: .comment}
>
> 1. {% tool [FASTQ to FASTA](toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.5) %} with the following parameters:
> 1. {% tool [FASTQ to FASTA](toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.2+galaxy2) %} with the following parameters:
> - {% icon param-collection %} *"FASTQ file to convert"*: `output collection` (output of **FASTQ Groomer** {% icon tool %})
> - *"Discard sequences with unknown (N) bases"*: `no`
> - *"Rename sequence names in output file (reduces file size)"*: `no`
Expand All @@ -350,7 +350,7 @@ See in the introduction for explanations on the Reverse-Complement.
> <hands-on-title> Align and consensus </hands-on-title>
>
> 1. {% tool [Align sequences](toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0) %} with the following parameters:
> - {% icon param-collection %} *"Input fasta file"*: `output collection` (output of **Tabular-to-FASTA** {% icon tool %})
> - {% icon param-collection %} *"Input fasta file"*: `output collection` (output of **FASTQ-to-FASTA** {% icon tool %})
> - *"Method for aligning sequences"*: `clustalw`
> - *"Minimum percent sequence identity to closest blast hit to include sequence in alignment"*: `0.1`
>
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