diff --git a/client/src/views/DocumentationView.vue b/client/src/views/DocumentationView.vue
index 29c361c1..d39240e4 100644
--- a/client/src/views/DocumentationView.vue
+++ b/client/src/views/DocumentationView.vue
@@ -58,39 +58,7 @@ import SubTitle from '@/components/ui/SubTitle.vue'
Simply put, a dataset consists of per-site records of RNA modifications stored in a given
- bedRMod file. The bedRMod or EU (epitranscriptome unified data exchange) format is similar
- to the
- ENCODE bedMethyl
- format (BED9+2), but includes a header. The name (4th column) must conform to the
- MODOMICS
- nomenclature for the modification short name, and the score (5th column) is a
- site-specific measure of confidence.
-
-
- The bedRMod file is a tabulated count of base modifications from every sequencing read
- over each reference genomic position. It is a convenient representation of the information
- stored in the
- MM/ML tags
- in BAM alignment files. When aligning or basecalling, most recent software should output
- these tags. For more information, consult the
+ bedRMod file. For more information, consult the
Browse.
Columns with arrow signs can be sorted. Multiple columns can be sorted, this requires a
@@ -164,11 +133,11 @@ import SubTitle from '@/components/ui/SubTitle.vue'
compare dataset with your own data.
- A First select a given organism, then select up to 3
+ 1. First select a given organism, then select up to 3
reference dataset. Use the search bar (dataset dropdown) to narrow down your selection.
- B Select up to 3 dataset for comparison. You can also use
+ 2. Select up to 3 dataset for comparison. You can also use
your own data (bedRMod or BED format). BED files with more than 6 columns are cut down to
BED6.
- C Select the operation you want to perform on the dataset
- selected in A and B. The more dataset you select or the larger the dataset, the longer the
- query time. Records can be exported to CSV.
+ 3. Select the operation you want to perform on the dataset
+ selected in previous steps. The more dataset you select or the larger the dataset, the
+ longer the query time. Records can be exported to CSV.
@@ -190,17 +159,18 @@ import SubTitle from '@/components/ui/SubTitle.vue'
- Sci-ModoM is freely available, and does not require login or registration. Interested
- users can however register to propose new projects, and eventually upload dataset and
- attachments that are made publicly available to all users.
+ Sci-ModoM is freely available, and does not require login or registration. Interested users can however register to propose new projects, and eventually upload
+ dataset and attachments that are made publicly available to all users.
To create a new project, fill the template request form, accessible for logged-in users
- through User menu > Data > Project template. Add a new metadata sheet for each dataset
- that belongs to this project.
+ through User menu > Data > Project template. Add a new
+ metadata sheet for each dataset that belongs to this project.
@@ -231,9 +201,9 @@ import SubTitle from '@/components/ui/SubTitle.vue'
To add dataset to an existing project, fill the upload form (Upload bedRMod), accessible
- for logged-in users through User menu > Data > Dataset upload. Use the Attach BAM files
- form to upload attachments. Attaching BAM files to a given dataset allow users to access
- read-level information.
+ for logged-in users through User menu > Data > Dataset upload.
+ Use the Attach BAM files form to upload attachments. Attaching BAM files to a given
+ dataset allow users to access read-level information.
Dataset upload errors
@@ -247,7 +217,7 @@ import SubTitle from '@/components/ui/SubTitle.vue'
rel="noopener noreferrer"
>bedRMod format specification. Pay particular attention to the header, which must meet strict requirements. Most
- errors are due to a badly formatted header, or a mismatch between a header tag, value pair
+ errors are due to a badly formatted header, or a mismatch between a header tag-value pair
and a corresponding value that you entered when filling the upload form. Most of these
errors can be resolved quickly without the need to contact us.
@@ -262,10 +232,9 @@ import SubTitle from '@/components/ui/SubTitle.vue'
too many contigs/scaffolds (only chromosomes are used)
wrong modification name (4th column)
mismatch between the modification name (4th column) and that chosen at upload
-
too many rows with undefined strand (6th column)
- too many rows with out-of-range values for score (5th column) or frequency (11th
- column)
+ too many rows with out-of-range values e.g. score (5th
+ column) or frequency (11th column)
@@ -273,7 +242,7 @@ import SubTitle from '@/components/ui/SubTitle.vue'
If you get a