How to convert the process radtags log to a tsv

[Edie Nissen]

Hello, I am very new to STACKS, and just completed my process_radtags run. Everything seems to have run smoothly, however I was wondering if there was a script to convert the process_radtags log into a tsv file. More specifically, I want to convert the data under per_barcode_raw_read_counts to run some analyses in R (which is suggested in the paper written by Rivera-Colón & Catchen, 2021 under section 2.4.1). Please let me know if you can help.

Thanks,

Edie

[Catchen, Julian]

Hi Edie,

 

The process_radtags.log file is a tab-separated file (with some sections of the file separated by blank lines). To make it easy to extract particular things from the file, use the stacks-dist-extract utility, which is included in the Stacks install. If you run it on the log file, it will tell you what you can extract:

 

stacks-dist-extract process_radtags.log 

per_file_raw_read_counts

total_raw_read_counts

 

You can then select one of the sections and extract that:

 

stacks-dist-extract process_radtags.log per_file_raw_read_counts

 

That is best for R. If you want it to print things out in human-readable table, do:

 

stacks-dist-extract --pretty process_radtags.log per_file_raw_read_counts

 

Best,

 

julian

[Edie Nissen]

Thanks for the reply!

Does this command create an output file for me to then use in R? Or am I able to use the whole populations.log file in R

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Stacks website: http://catchenlab.life.illinois.edu/stacks/
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Edie Nissen (she/her)

Biology M.S. Student

Department of Applied Ecology

North Carolina State University

[Catchen, Julian]

Redirect the output into a file for use in R:

 

stacks-dist-extract process_radtags.log per_file_raw_read_counts > myRfile.tsv

[Edie Nissen]

Awesome. Thanks so much for the help!

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