Modules/QC.md

@@ -29,8 +29,23 @@ Contamination during sequencing experiment is unavoidable. Thus, it's necessary
 
 fastQscreen process one fastq file at once. Therefore, for paired-end data, fastQscreen will be run three times (<samples>_R1.filtered.fq, <samples>_R2.filtered.fq, <samples>_unpaired.filtered.fq). This may lead to newly unpaired reads between R1 and R2 and required an additional step to extract those reads from R1 or R2 and to add them to the unpaired file. This step is performed using [repair utility](https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/repair-guide/) from the bbtools suit.
 
+## Merging ##
+
+In case of paired-end data , Reverse and forward reads might be merged. This is done after the QC and contaminant removal. Reads that fail to merge remain in their respective file whereas merged reads are stored within the unpair file.
 
 ------
 ------
 
+Raw reads and processed reads are stores within the reads directory :
+reads/
+└── PE
+    ├── ESM5MEBG
+    │   ├── ESM5MEBG_R1 -> /ceph-recherche/shares/genosysmics/sample/ESM5MEBG_R1.fastq.gz *symlink
+    │   ├── ESM5MEBG_R1.filtered.fastq.gz
+    │   ├── ESM5MEBG_R2 -> /ceph-recherche/shares/genosysmics/sample/ESM5MEBG_R2.fastq.gz *symlink
+    │   ├── ESM5MEBG_R2.filtered.fastq.gz
+    │   └── ESM5MEBG_unpaired.filtered.fastq.gz
+    └── ...
+
+
 ![dag_qc.svg](uploads/957ffb7b53f8ef601a141db07b91dabf/dag_qc.svg)