Shaun Jackman
Shaun Jackman
This feature is now implemented in the utility `tigmint-molecule`. See https://github.com/bcgsc/tigmint The input BAM file must be sorted by barcode and position using `samtools sort -tBX`.
You can use `samtools fastq -TBX` for this purpose.
> The --cookbook option (no examples yet) allows for this. I've found with Homebrew that its nice to include the cookbook in the identifier. For example, `brew install homebrew/science/abyss` fetches...
> Worth considering, though I was fearful of confusion with real directories. It's really nice to be able to paste from the terminal/command line into the browser location without having...
> That said, if just /foo/bar/recipe are given on the CL, it could assume a github base by default. Yes, and if a full URL is given, use that, which...
Good to know. I'm going to give it a stab with `numpy==1.9.1` and `h5py==2.4.0`.
It's produced by [BFC](https://github.com/lh3/bfc).
Yes, the first record is always the first read of the pair / mate-pair. FR orientation for PE and RF orientation for MP. Good suggestion. If there's no easy workaround...
I instead aligned the reads using `bwa mem` ``` sh bwa mem -t32 -p contigs.fa reads.fa.gz | samtools view -F2304 -b -o reads.bam - ```
I did at first, and I had suspected that's what had gone wrong. But, no, I repeated the estimates with `--mle` and got the same error.