Find adapter sequences

Question

[science_lizard]

Hi all - So, I know which adapters I put on each sample, but the tubes got mixed up before I could label them. I went ahead with sequencing but I now need to determine which sample is which. Ordinarily, I would just use FastQC to identify adapter sequences, but none are showing up in the report (possibly because these are custom adapters). A friend of mine told me to convert my fastq files to fasta, then use bowtie to find how many times the adapter sequence comes up in the file, but I can't figure out how to do that (although I have converted the files to FASTAs). Anyone know how I might be able to do this, or know another way of determining which sample was labeled with each adapter?

Thanks!

[h.mon]

Please provide some more detail:

Did your samples get split into different files?

Could you describe your "custom adapters"? Do you mean instead of using Illumina adapters + barcodes, you used custom built adapters + barcodes? What identifies each sample are the barcodes, not the adapters. Where your custom barcodes are expected expected to be located? Inline with the reads, or inside the adapters?

edit: if the barcodes are inline with the sequencing reads, you could use bbduk with the literal= parameter.