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Initialize

Prepare directories

Create a working directory and subdirectories:

mkdir DTEG
cd DTEG
mkdir FASTQ
mkdir HTSeq

Create a subdirectory for each sample. Example:

mkdir FASTQ/HEK_WT1
mkdir FASTQ/HEK_WT2
mkdir FASTQ/HEK_ThumD_KO1
mkdir FASTQ/HEK_ThumD_KO2
mkdir FASTQ/HEK293ThumpD1KO1RNA
mkdir FASTQ/HEK293ThumpD1KO2RNA
mkdir FASTQ/HEK293WT1RNA
mkdir FASTQ/HEK293WT2RNA

Index

You can link the pre-made index folder for hg19 in the working directory:

ln -s /mnt/rnabl-work/Guiblet/CCBRRBL8/NextFlow ./

You can create a new index as follow: TBA

Scripts

Download the following files in the working directory:

Open the nextflow.config file and change /mnt/rnabl-work/Guiblet/CCBRRBL8/NextFlow/ to your working directory (full path)

Sample Info

Create the sample_info.txt as the following example:

SampleID        Condition       SeqType Batch
HEK_WT1 1       RIBO    1
HEK_WT2 1       RIBO    2
HEK_ThumD_KO1   2       RIBO    1
HEK_ThumD_KO2   2       RIBO    2
HEK293WT1RNA    1       RNA     1
HEK293WT2RNA    1       RNA     2
HEK293ThumpD1KO1RNA     2       RNA     1
HEK293ThumpD1KO2RNA     2       RNA     2
Last update: 2023-01-31