Sample Name list generator - AndreaRP/METAGENOMICS GitHub Wiki

To get the sample name of each of your samples you can run [samplesID_gen.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/samplesID_gen.sh)

Usage

bash samplesID_gen.sh

Note that you should have placed all the read files in ANALYSIS/00-reads for this script to work.

In a nutshell...

• 1. Gets the sample name from the file names in 00-reads folder. Given raw read files with the following name structure:
• sampleName_*R1*.fastq.gz
• sampleName_*R2*.fastq.gz

The sample name will be the word before the first underscore ('_') in the read file name.

I/O

• Input Files (In ANALYSIS/00-reads/)

  • sampleName1_*R1*.fastq.gz
  • sampleName1_*R2*.fastq.gz
  • sampleName2_*R1*.fastq.gz
  • sampleName2_*R2*.fastq.gz
  • sampleName3_*R1*.fastq.gz
  • sampleName3_*R2*.fastq.gz
  • ...
  • sampleNameN_*R1*.fastq.gz
  • sampleNameN_*R2*.fastq.gz

• Output Files (in ANALYSIS/)

  • samples_id.txt: File containing a list with the name of each sample.