You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: docs/marker_gene.md
+14-13Lines changed: 14 additions & 13 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -7,7 +7,7 @@ header_type: base
7
7
permalink: /docs/marker-gene/
8
8
---
9
9
10
-
> This page is currently still a work in progress. You can see the current version on our [Github Wiki](https://github.com/LangilleLab/microbiome_helper/wiki/Microbiome-Helper-2-Marker-gene-workflow).
10
+
> <iclass="fa-solid fa-circle-info"></i> This page is currently still a work in progress. You can see the current version on our [Github Wiki](https://github.com/LangilleLab/microbiome_helper/wiki/Microbiome-Helper-2-Marker-gene-workflow).
@@ -32,7 +32,7 @@ To standardize QIIME 2 analyses and to keep track of provenance (i.e. a list of
32
32
33
33
## 1. First steps
34
34
35
-
> It is assumed that you already have a folder containing your raw data that is called `raw_data/`. This will contain either single- or paired-end reads. I would recommend creating this inside a folder that describes your project - if you are using the [tutorial data](https://github.com/LangilleLab/microbiome_helper/wiki/Microbiome-Helper-2-Tutorial-data), then this could be inside a folder called `arctic_ocean_illumina` or `arctic_ocean_pacbio` so that you have *e.g.*, `arctic_ocean_illumina/raw_data`
35
+
> <iclass="fa-solid fa-circle-info"></i> It is assumed that you already have a folder containing your raw data that is called `raw_data/`. This will contain either single- or paired-end reads. I would recommend creating this inside a folder that describes your project - if you are using the [tutorial data](https://github.com/LangilleLab/microbiome_helper/wiki/Microbiome-Helper-2-Tutorial-data), then this could be inside a folder called `arctic_ocean_illumina` or `arctic_ocean_pacbio` so that you have *e.g.*, `arctic_ocean_illumina/raw_data`
36
36
{: .alert .alert-info .p-3}
37
37
38
38
It is also assumed that these reads are in demultiplexed FASTQ format. QIIME 2 accepts many different formats so if your files are not already in this format (e.g. not demultiplexed) you would just need to use slightly different commands for importing your data.
@@ -61,7 +61,7 @@ Visualize sequence quality across raw reads. This is important as a sanity check
61
61
62
62
This is an important step for identifying outlier samples with especially low quality, read sizes, read depth, and other metrics.
63
63
64
-
> Note that we don't actually show the steps for removing any samples here. There are other steps later on where low-quality sequences will be removed, however, if a large number of your samples show very low quality here, this may be an indication that something went wrong with your sequencing and you may want to investigate this further before carrying on with your analysis.
64
+
> <iclass="fa-solid fa-circle-info"></i> Note that we don't actually show the steps for removing any samples here. There are other steps later on where low-quality sequences will be removed, however, if a large number of your samples show very low quality here, this may be an indication that something went wrong with your sequencing and you may want to investigate this further before carrying on with your analysis.
65
65
{: .alert .alert-info .p-3}
66
66
67
67
You can run FASTQC with this command (after creating the output directory).
@@ -99,37 +99,38 @@ If you are working from the directories/folders that we have suggested, this wil
> If you are using the tutorial data that we have provided then you will need to run the following commands to make a new metadata file that has the column names that QIIME2 is expecting, in the right place:
102
+
> <iclass="fa-solid fa-circle-info"></i> If you are using the tutorial data that we have provided then you will need to run the following commands to make a new metadata file that has the column names that QIIME2 is expecting, in the right place:
sed -i 's/sample_rename/sampleid/g' arctic_study_metadata.txt
107
108
```
108
109
These commands are: (1) removing the first column, and (2) renaming the first column from `sample_rename` to `sampleid`.
109
110
110
-
> Note that we don't actually use this metadata file in the workflow shown on this page! It is used in the next step (QIIME2 statistics and visualisation) and it is always a good idea to have an idea of what your samples are so that you can interpret things about them more easily, but if you don't have one made at this point then that is not a deal-breaker!
111
+
> <iclass="fa-solid fa-circle-info"></i> Note that we don't actually use this metadata file in the workflow shown on this page! It is used in the next step (QIIME2 statistics and visualisation) and it is always a good idea to have an idea of what your samples are so that you can interpret things about them more easily, but if you don't have one made at this point then that is not a deal-breaker!
111
112
{: .alert .alert-info .p-3}
112
113
113
-
> A primary alert
114
+
> <iclass="fa-solid fa-circle-exclamation"></i> A primary alert
114
115
{: .alert .alert-primary .p-3}
115
116
116
-
> A secondary alert
117
+
> <iclass="fa-solid fa-bell"></i> A secondary alert
117
118
{: .alert .alert-secondary .p-3}
118
119
119
-
> A green alert
120
+
> <iclass="fa-solid fa-bell"></i> A green alert
120
121
{: .alert .alert-success .p-3}
121
122
122
-
> A warning
123
+
> <iclass="fa-solid fa-triangle-exclamation"></i> A warning
0 commit comments