Commit 3e5290ec authored by peguerin's avatar peguerin
Browse files

README installation update

parent bd1ba812
......@@ -104,7 +104,7 @@ let's define some wildcards `*`
- `{pool}` : any pools into a run
- `{species}` : any species
* [config.yaml](01-info_files/config.yaml) :
* [config.yaml](01-info_files/config.yaml) : defines a dictionary of configuration parameters and their values used on each step commands of the pipeline.
* [barcodes.txt](01-info_files/barcodes.txt) : file containing barcodes used for {pool} into {run}
* [{species}_infos.csv](01-info_files) : information `.csv` table related to {species} each row is a sample and they are 4 columns which are run,pool,barcode,ID
* [{species}_populations_map.txt](01-info_files) : information table `.tsv` related to {species}. Each row is a sample and they are 2 columns which are ID,population. This file can be generated by the pipeline (see [Configuration](#42-configuration) section). However we strongly recommand you to do it manually.
......@@ -140,7 +140,7 @@ You will see the following folders :
```
* [03-samples](03-samples): will store the results generated by demultiplexing with [process_radtags](http://catchenlab.life.illinois.edu/stacks/comp/process_radtags.php) and clone filtering [clone_filter](http://catchenlab.life.illinois.edu/stacks/comp/clone_filter.php). The data must be stored this way :
```
02-raw/
03-samples/
runA/
poolA1/
sample_{barcode1}.1.fq.gz
......@@ -181,7 +181,7 @@ You will see the following folders :
```
* [04-all_samples](04-all_samples): paired end `fastq.gz` files are named according to [{species}_infos.csv](01-info_files) information. Then reads are aligned onto reference genome sequences stored into [08-genomes](08-genomes). This folder contains "named" fatsq files and corresponding alignments `.bam` files. `.sorted.bam` are SORTED alignment files and `.sorted.bam.bai` are corresponding index. The data must be stored this way :
```
02-raw/
04-all_samples/
speciesA/
{sampleA1}.1.fq.gz
{sampleA1}.2.fq.gz
......
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