Stacks: Using trimmed sequences as input for de novo map?

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Hello! I am trying to assemble a de novo genome map from SNP data. The program runs on my raw reads (fastq files), but these reads are not the best quality. I trimmed them using Trimmomatic to improve their quality, but now de novo map won’t accept the output files from trimmomatic as input:

{ “code_desc”: “Error in Stacks execution”, “desc”: “Fatal error: Exit code 255 (Error in Stacks execution)”, “error_level”: 3, “exit_code”: 255, “type”: “exit_code” }

I checked that they are still in fastq format. Any ideas on how I can solve this?? Thanks!

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Hi @melissajbetters

That tool suite has a lot of components, and some are required to be run before others. The sequence IDs are used as sample IDs that are cross referenced (and presumably required to be present). If that sounds like what is going on – you might need to rerun some steps.

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Original poster here- Just wanted to let others know for future reference that I solved this issue. Stacks does not accept Trimmomatic outputs as inputs. However, the Stacks pipeline is constructed such that quality filtering can be performed directly within the process_radtags function. Hope this helps others:)

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