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johnlees
sequence element (kmer) enrichment analysis
Hi there, I am following the tutorial using my own batch of genomes (>600 bacterial genome sequences approx 3.5Mb each). For four days now I am stuck at the step:...
Makes plots easier from output, and current header incorrectly has MAF when AF is displayed.
Hard to set a sensible default, require scree plot to be used
It would be more general to allow any order of sam file, by using the k-mer as a unique ID between the SEER output and mapping co-ordinates.
If you use the command: for i in $(find . -name stdout); do filter_seer -k $i --pos_beta | sed '1d' >> seer_filtered.txt; done as in the tutorial, the file that...
This may not be critical but happens a lot with C++ builds: ``` ../dlib/dlib/matrix/../smart_pointers/shared_ptr.h:299:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr& r ^ In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/memory:81:0, from...
It prints the help, then it pauses for 1 second, then it dumps core. The `kmds` command does the same thing. Downloaded from: https://github.com/johnlees/seer/releases/download/v1.1.3/seer_v1.1.3_static_all.tar.gz The same happens with the `_static`...
Need to use a machine with cmake 2.7.12 or above. Setting "dist": "trusty" in .travis.yaml might work, but need to test. For now workaround in ca03e4d07b391a4bb89e6efe50565a59b2ca8891
Hi, I've encountered an error with map_back with respect to threading. The error files reads: map_back: tpp.c:63: __pthread_tpp_change_priority: Assertion `new_prio == -1 || (new_prio >= __sched_fifo_min_prio && new_prio
Try using BOBYQA algorithm to maximise likelihood for Firth regression, rather than N-R iterations. I wonder if it might be faster...