Concatenation of process_radtags output sample files

[Paulo Buckup]

I have double-digested paired-end Illumina reads. The library was prepared so that R1 contains one enzyme cut site, and R2 contains the other enzyme cut site. I have been running the denovo_map.pl script (with the--paired option) without concatenating the four files produced by process_radtags.pl for each sample. 

However, step 11 in the protocol published by Rochette & Catchen (2017) states that these four files should be concatenated:

"11| If you are working with paired-end sequencing data, concatenate, for each sample, the four files of reads produced by process_radtags (<sample name>.1.fq.gz, <sample name>.rem.1.fq.gz, <sample name>.2.fq.gz, and <sample name>.rem.2.fq.gz).

% cp sample_name.1.fq.gz sample_name.fq.gz
% cat sample_name.2.fq.gz > sample_name.fq.gz
% cat sample_name.rem.1.fq.gz > sample_name.fq.gz
% cat sample_name.rem.2.fq.gz > sample_name.fq.gz"

So, here are my questions:

1. Why is this concatenation necessary?

2. What happens to my catalog if these files are not concateneted?

Thanks,

Paulo Buckup

[Catchen, Julian]

Hi Paulo,

 

You don’t need to concatenate those files together if working with Stacks v2. Stacks v1 did not understand paired-end data natively, but v2 does. You might consider our newer protocol which covers similar ground but is written around v2:

 

https://link.springer.com/protocol/10.1007/978-1-0716-2313-8_7

 

Best,

 

julian

[Paulo Buckup]

Thanks!

Paulo Buckup

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
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