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Before doing your analysis, you should transfer the FASTQ files into your project folder /shared/projects/YourProjectName
.
EDC workflows are expecting gzip-compressed FASTQ files with names formatted as
SampleName_R1.fastq.gz
and SampleName_R2.fastq.gz
for pair-end data,SampleName.fastq.gz
for single-end data.If your files are not fitting this format, please see how to correct the names of a batch of FASTQ files.
It is highly recommended to check the md5sum for big files. If your raw FASTQ files are on your computer in PathTo/RNAseqProject/Fastq/
, you type in a terminal:
You@YourComputer:~$ cd PathTo/RNAseqProject
You@YourComputer:~/PathTo/RNAseqProject$ md5sum Fastq/* > Fastq/fastq.md5
You can then copy the Fastq
folder to the cluster using rsync
, replacing username
by your login:
You@YourComputer:~/PathTo/RNAseqProject$ rsync -avP Fastq/ username@core.cluster.france-bioinformatique.fr:/shared/projects/YourProjectName/Raw_fastq
In this example the FASTQ files are copied from PathTo/RNAseqProject/Fastq/
on your computer into a folder named Raw_fastq
in your project folder on IFB core cluster. On iPOP-UP cluster, only the address is different:
You@YourComputer:~/PathTo/RNAseqProject$ rsync -avP Fastq/ username@ipop-up.rpbs.univ-paris-diderot.fr:/shared/projects/YourProjectName/Raw_fastq
Feel free to name your folders as you want! You will be asked to enter your password, and then the transfer will begin. If it stops before the end, rerun the last command, it will only add the incomplete/missing files.
After the transfer, connect to the cluster (IFB, iPOP-UP) and check the presence of the files in Raw_fastq
using ls
command.
[username@clust-slurm-client YourProjectName]$ ls Raw_fastq
Check that the transfer went fine and that all files are complete using md5sum
.
[username@clust-slurm-client YourProjectName]$ cd Raw_fastq
[username@clust-slurm-client Raw_fastq]$ md5sum -c fastq.md5
Author : Magali Hennion
Last update : 26/10/2023
BiBs
2024 parisepigenetics
https://github.com/parisepigenetics/bibs |
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s |
focus search bar ( enter to select, ▲ / ▼ to change selection) |
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g f |
go to facility |
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go to guidelines |
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toggle this help ( esc also exits) |