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mcveanlab / mccortex

De novo genome assembly and multisample variant calling
https://github.com/mcveanlab/mccortex/wiki
MIT License
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Creating cortex graph from more than two FASTQ files #65

Closed winni2k closed 6 years ago

winni2k commented 6 years ago

I have two paired-end FASTQ files and two unpaired FASTQ files from the same sequencing run (output from trimmomatic). I would like to create a single graph from all of these files. So far I have tried to create three separate graphs (one for the paired-end reads, and two for the single end reads), but I can't figure out how to merge the three graphs into one using only one color. Using the join command gives me one graph with three colors, but I want all data to be merged into one color.

Is this possible with mccortex?

noporpoise commented 6 years ago

Using the offset notation, you can load each graph into colour zero:

mccortex join out.ctx 0:in1.ctx 0:in2.ctx 0:in3.ctx

The syntax is briefly described here: https://github.com/mcveanlab/mccortex/wiki/Join-command

noporpoise commented 6 years ago

I'm closing for this issue for now - please re-open or comment if it's not clear.

winni2k commented 6 years ago

Ah! Great. I'm adding this example to the wiki page because I think that might be helpful.