Fastqsanger to fastq

Hi all,

I got paired-end .fastq files from Genewiz Ampicon EZ service.
Then I try to de-multiplex the files by the barcodes (in my primers) by the Barcode Splitter tool.
However, that tool returned my .fastqsanger files instead of .fastq format.

Because I want to use CRISPResso2 (CRISPResso2) to analyze my result and CRISPRresso only recognize .fastq format. Does anybody have experience converting .fastqsanger to .fastq?

I have tried Fastq Groomer tool and Fastq-sanger to Fastq Sequence Converter (
But they dont seem to help, the resulting files still cannot be recognized by CRISPResso.

Hi @Woofung,
could you provide me the output of FastQC on your samples? Usually the extension doesn’t provide so much information about the specific fastq encoding version. I think there should be some additional problem since the example sequences provided by the developers are fastqsanger (Sanger / Illumina 1.9).


Hi gallardoalba,

Thanks for the help.
I am new to this field, and I am not sure if this is what you were asking for.
I run the FastQC for the file I upload to split:

This is the split file that I received.

Yes, your sequences are in fastqsanger format. You should be able to use them with CRISPesso2, since as I mentioned you previously, the test datasets provided by CRISPesso2 developers (e.g.nhej.r1.fastq.gz) are fastqsanger too, despite having the fastq file extension.

Screenshot from 2021-04-25 18-24-51


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