Question: cutadapt, barcode splitter and merging files
gravatar for anujaasathe
4.7 years ago by
anujaasathe0 wrote:

Apologies if this has been asked before. I am a beginner at NGS analysis and could not find anything similar. 

I am dealing with 4 fastq files: 2 runs each with a single and paired end file. They contain 3 multiplexed PCR  amplicons. I used the barcode splitter from the FASTX toolkit to demultiplex them and  it worked well.  I next want to use cutadapt to trim primers. However, when using cutadapt on the files generated after the demultiplexing, I  get an error that this cannot be performed as the files might be truncated. My questions are as follows:

1. Is something wrong with the format of the files after using the barcode splitter? Can I fix this?

2. Ideally,  I want to work with a single merged file and sort relevant data (half of  the single and paired end reads are likely to be useful for my purpose). I am not sure if I can simply merge 2 different runs with single and paired reads into one file. The other option would be to run the barcode splitter  individually on the 4 files. Then combine the resulting files belonging to one barcode together from both runs and reads.  How do I go about this?

Thanks for the time and all advice will be much appreciated. 

next-gen software error • 2.3k views
ADD COMMENTlink modified 4.7 years ago by genomax91k • written 4.7 years ago by anujaasathe0
gravatar for genomax
4.7 years ago by
United States
genomax91k wrote:

It is hard to answer question #1 since in an ideal situation demultiplexing with fastx_barcode_splitter should produce files with proper format.

You may want to look at sabre which can do demultiplexing and trimming of the internal barcodes for SE and PE data.

ADD COMMENTlink written 4.7 years ago by genomax91k
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