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I was wondering if it is possible to get the Greengenes reference sequence ID used to assign taxonomy to the sequence variants inferred by dada2. This information is useful for other pipelines such …
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Hi,
I'm trying to run Tracer on my work cluster. It seems to run fine up until the part where it is quantifying with kallisto (or perhaps just after). Below is the last part of the error message. A…
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Hi @noporpoise,
I'm running mccortex building and cleaning on a bunch of samples from the ENA and a small percentage are failing on the cleaning step without much information as to why.
Here's…
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Given the strange results I've been getting with kevlar, I felt I had no choice but to compute exact k-mer counts for one of my human samples, compare these exact counts to the approximate counts give…
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What are the recommended defaults for the following options:
```
--min_kmer_frac MIN_KMER_FRAC
--max_kmer_frac MAX_KMER_FRAC
--kmer_count KMER_COUNT
--start_gene_id START_GENE_ID
--start_ge…
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@vdauwera commented on [Sat Mar 07 2015](https://github.com/broadinstitute/gsa-unstable/issues/855)
#### Issue description / case details
Users who are dealing with large ploidies (typically for poo…
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Hi Jared (and colleagues),
I have recently put a genome together and want to see if there is evidence for methylation. A previous paper reported some evidence using an antibody on polytene chromoso…
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```
ano@ano-svr1:~$ adam-submit -version
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using SPARK_SUBMIT=/home/ano/app/spark-2.0.1-bin-hadoop2.6/bin/spark-submit
Spark Command: /usr/lib/jvm/ja…