Closed roddypr closed 6 years ago
Hi, I wonder if you've had time to take a look at this issue! Best wishes, Roddy
To use the information from paired reads you need to use threading. See "Read Threading" on this page: https://github.com/mcveanlab/mccortex/wiki/Workflow-Examples#ReadThreading
Thanks @benjeffery. So, paired reads are treated as single end reads during graph construction, right? Then, why not build two graphs using --seq
option: one for forward and one for reverse reads, instead of specifying both with --seq2
option? Is this information stored in the graph somehow and used in the read threading step?
Apologies for the late response. McCortex graph construction is a multi-step process. make-pipeline.pl
is designed to run all these steps for you. The steps are:
The final output is a de bruijn graph (.ctx
file) and a corresponding links file (.ctp
file)
I'm unclear which step the output you posted is from. The graph construction has no notion of forward/reverse reads - I may have misunderstood what you meant there. Hopefully I've answered your questions - please re-open the issue if not.
Thanks, @noporpoise. Yes, that answers our questions. The output we posted was from mccortex build
command.
Hi,
I'm running mccortex using make-pipeline.pl.
I have an example where I have three batches of paired-end sequences for the same individual. I've noticed that the log file for the initial graph building says that all reads are read as single-ended reads. @yeban has seen the same issue in his runs of mccortex as well.
Is this correct?
Best wishes,
Roddy
The entries for the remaining input files all say
SE reads: 0 PE reads: 0
.