marcelm / marcelm/cutadapt

Ensuring to find the correct file after Demultiplexing my 16S amplicon raw dataset with combinatorial dual indexes cutadapt command

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Python
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Description

  • Cutadapt and Python version used: 4.8
  • The method you used to install the tool (conda or pip, for example): Used mamba
  • The command-line parameters you used for demultiplexing paired-end reads with combinatorial dual indexes cutadapt command:
cutadapt \
    -e 0.15 --no-indels \
    -g ^file:barcodes_fwd.fasta \
    -G ^file:barcodes_rev.fasta \
    -o {name1}-{name2}.1.fastq.gz -p {name1}-{name2}.2.fastq.gz \
    input.1.fastq.gz input.2.fastq.gz

Here are some of the output generated from the code above:

LIB1_sample_189-LIB1_sample_183.1.fastq.gz
LIB1_sample_189-LIB1_sample_183.2.fastq.gz
LIB1_sample_189-LIB1_sample_184.1.fastq.gz
LIB1_sample_189-LIB1_sample_184.2.fastq.gz
LIB1_sample_189-LIB1_sample_185.1.fastq.gz
LIB1_sample_189-LIB1_sample_185.2.fastq.gz
LIB1_sample_189-LIB1_sample_186.1.fastq.gz
LIB1_sample_189-LIB1_sample_186.2.fastq.gz
LIB1_sample_189-LIB1_sample_187.1.fastq.gz
LIB1_sample_189-LIB1_sample_187.2.fastq.gz
LIB1_sample_189-LIB1_sample_188.1.fastq.gz
LIB1_sample_189-LIB1_sample_188.2.fastq.gz
LIB1_sample_189-LIB1_sample_189.1.fastq.gz
LIB1_sample_189-LIB1_sample_189.2.fastq.gz
LIB1_sample_189-LIB1_sample_190.1.fastq.gz
LIB1_sample_189-LIB1_sample_190.2.fastq.gz
  1. What is the correct combination of fastq.gz files for further analysis? I have a total of 230 samples.
  2. How can I pick those right files from the combination pool folder?

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with Cutadapt's documentation for demultiplexing paired-end reads and combinatorial dual indexes, then reproduce the supplied command on a small input subset. Compare the generated paired filenames with the barcode combinations and document how valid pairs can be identified and selected for all samples.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Documentation
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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