Instructions for uploading data to the server

Before running the pipeline, first upload the input file to the server as follows:

Press on the “choose files” button, and select the root folder of the files

Uploading folder of fastq files

Fastq files must be organized, within the selected folder (root folder), into subfolders as shown below. Subfolders names are derived from sample names.
Each subfolder contains the relevant fastq file, which can be compressed into the “gz” format.
Fastq file names must end with “_R1.fastq(.gz)” or “_R1.fq(.gz)” for single-read data. The “R” prefix denotes the read number.
In the case of paired-end data (required for Mars-Seq), corresponding files must exist, with suffix “_R2.fastq(.gz)” instead of “_R1.fastq(.gz)”.

For example:

root folder
- sample1
  
  sample1_R1.fastq
  
  sample1_R2.fastq (must exist in Mars-seq and in paired-end)
- sample2
  
  sample2_R1.fastq
  
  sample2_R2.fastq (must exist in Mars-seq and in paired-end)

The pipeline also supports the old convention of the fastq file names _L00*_R1_0.fastq. The letter “L” denotes the lane number, “R” denotes the read number, and the numbers 001,002 etc denote serial number of the file for each lane and read

For example:

root folder
- sample1
  
  sample1_S0_L001_R1_001.fastq
  
  sample1_S0_L001_R1_002.fastq
  
  sample1_S0_L002_R1_001.fastq
  
  sample1_S0_L002_R1_002.fastq
  
  sample1_S0_L001_R2_001.fastq
  
  sample1_S0_L001_R2_002.fastq
  
  sample1_S0_L002_R2_001.fastq
  
  sample1_S0_L002_R2_002.fastq
- sample2
  
  …

Uploading input for the demultiplexing pipeline

For the pipeline of demultiplexing from BCL files: upload the original bcl folder. The original folder name should adhere to the template: <date>_<field2>.<field3>_field4>, e.g. 180514_NB551168_0123_AHTHHKBGX5.
For the pipeline of demultiplexing from FASTQ files: upload the folder containing the undetermined FASTQ files. Note: the pipeline can process multiple files per read as input (e.g., multiple files for each R1 and R2, such as undetermined_fastq_files/Undetermined_S0_L001_R1_001.fastq.gz and Undetermined_S0_L002_R1_001.fastq.gz).