Map barcode to gene

Question

[Jinsoul]

I'm a wet lab scientist with minimal coding skills. I made a library to barcode different genes and sent an amplicon that includes the gene and the barcode for Illumina paired-end sequencing and we'll receive the fastq files.

We alredy have the sequences for the genes, we just need to know the sequences of barcodes (18bp) that go with each gene, are there alredy any tools that can do this?

[GenoMax]

Just saying you have a 18bp barcode is not enough information. You will need to tell us something more about the actual construct and where you expect the barcode to be. You obviously are not sequencing a full length gene amplicon with Illumina sequencing so how did you make the libraries.

Besides the tool mentioned below you may also be able to use sabre: https://github.com/najoshi/sabre

[Jinsoul]

Sorry, the amplicon we sent: 5`- Last 300 bp of gene - Constant region 20 bp - Random unknown 18bp barcode - Constant region 30 bp - 3'.

Answer 1

[size_t]

this maybe useful to you : split pooled paired-end fastq using fqkit