Jared Simpson
Jared Simpson
Great, thanks @tijyojwad and @shenker
Hi @ParsaAkbari, It looks OK to me? https://github.com/jts/nanopore-paper-analysis/blob/master/full-pipeline.make#L193 Jared
What I meant is that the code that I linked to in step 5 looks correct (the prereq is draft_genome.fasta) : ``` # index the draft assembly for bwa draft_genome.fasta.bwt:...
Regarding reads.corrected.corrected.fasta: the Makefile is correct, we perform two rounds of error correction. Regarding the path to CA: we set the PATH environment variable so the full path does not...
Sorry I missed this earlier. The number of POA processes that are run in parallel will be exactly the CORES argument. Note that the pipeline script is for a single...
Hi Parsa, The command line argument (CORES=xx) will override the default value in the Makefile. Jared On Tue, Jan 19, 2016 at 5:58 AM, Parsa Akbari [email protected] wrote: > I...
If I did not specify these versions, pip would fail to install subsequent packages. It may be my environment
Ok, let me know how it goes.
Hi Ariel, The `configure` script is automatically generated by `autoconf` from the input file `configure.ac` - you should not have to edit it directly. What error messages does `./configure --with-bamtools=/path/to/lib`...
Hi Ariel, I'm just back from a trip, sorry for the slow response. Can you show the contents of your bamtools directory? ``` ls /n/core/Bioinformatics/analysis/Yu/4MB_resequencing/Sanger/bams_20150923/strains_16/peaks_realignment/assembly/SGA/bamtools/ ```