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Fixing references to barcode-whitelist #122

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Fixing references to barcode-whitelist #122

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014cf5c
Fixing references to barcode-whitelist
mys721tx Jan 5, 2025
29e2c08
Fixing table columns
mys721tx Jan 5, 2025
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6 changes: 3 additions & 3 deletions docs/docs/Create-config-files.md
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ META:
reference-directory: /path/to/references/
gtf_biotypes: gtf_biotypes.yaml
FILTER:
barcode_whitelist: ''
barcode-whitelist: ''
5-prime-smart-adapter: AAAAAAAAAAA
cell-barcode:
start: 1
Expand Down Expand Up @@ -88,7 +88,7 @@ Please note the "space" after the colon, is needed for the yaml to work.
* `gtf_biotypes` is the gtf_biotypes.yaml file containing the selection of biotypes you want to keep for your gene to read attribution. Using less biotypes may decrease your multimapping counts.

### [FILTER]
* `barcode_whitelist` is the filename of your whitelist fi you have one. Well plate base protocols often have one.
* `barcode-whitelist` is the filename of your whitelist fi you have one. Well plate base protocols often have one.
* `5-prime-smart-adapter` is the 5" smart adapter used in your protocol.
* `cell-barcode and UMI-barcode`: Is the section for cell/umi barcode filtering.
* `start` is the first base position of your cell/umi barcode.
Expand Down Expand Up @@ -137,7 +137,7 @@ This file holds the sample names, expected cell numbers and read length for each
The file has to have this format:

```
samples,expected_cells,read_lengths,batch
samples,expected_cells,read_length,batch
sample_name1,500,100,Batch1
sample_name2,500,100,Batch2
```
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2 changes: 1 addition & 1 deletion docs/docs/Running-dropSeqPipe.md
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Expand Up @@ -76,7 +76,7 @@ In order to use this functionnality you just need to add a whitelist barcode fil

```
FILTER:
barcode_whitelist: name_of_your_whitelist_file
barcode-whitelist: name_of_your_whitelist_file
```
The file should be in the WORKING_DIR. Run the pipeline as usual.

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