process_radtags can't currently handle this case. It expects combinatorial
barcodes to be associated with paired-end reads. I'll update the code to handle
this case. If you don't have paired-end reads, it is also unnecessary to rename
the files to account for _R1_ and _R2_, obviously.
In the meantime, you could run process_radtags twice, first specifying the
inline barcodes, and then a second time on each output file (using -f to direct
it to each file produced in the first run), specifying the index barcodes
(giving --inline_null and --index_null as the command line option, respectively).
It will take me a day or two to write the new code.
On 6/4/13 3:07 PM,
john.h...@gmail.com wrote:
> What if I don't have paired-end reads? I.e., I have single reads indexed with
> "third"-reads, but no second read.
>
> I renamed my reads to follow your format:
> dataset_001_ATCACG_L001_R1_001.fastq.gz
> and so on for the other 12 combinatorial barcodes, for a total of twelve files.
> I gave it a list of barcodes, which was just
> inline_index <tab> combinatorial_index
> for every possible combination.
>
> Now it is dumping all of my reads as ambiguous. I looked in the log file, and
> it finds zero of the appropriate barcodes:
>
> /Barcode Total No RadTag Retained/
> /GCATG-ATCACG 0 0 0/
> /AACCA-ATCACG 0 0 0/
> /CGATC-ATCACG 0 0 0/
> /TCGAT-ATCACG 0 0 0/
>
> And only inline barcodes:
>
> /Sequences not recorded/
> /Barcode Total/
> /GAGTC 5744812/
> /GAGAT 5457263/
> /GCATG 5139967/
> /GTAGT 5130677/
> /GGCTC 4748589/
> /AACCA 4647654/
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--
Julian M Catchen, Ph.D.
Institute of Ecology and Evolution
University of Oregon
--
jcat...@uoregon.edu
http://www.uoregon.edu/~jcatchen/