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Calling `qiita_env make --add-demo-user --load-ontologies --download-reference` will fail with the following traceback:
``` python
File "/Users/yoshikivazquezbaeza/git_sw/qiita/scripts/qiita_env", …
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Hello,
We have several samples that were created using "Trusight RapidCapture Cancer Panel" on which I ran the default configuration of bcbio for variant calling (see example of the config below). …
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Hi!
I'm interested in using your variant caller in my pipeline and have already done a test run on targeted re sequencing data using the amplicon-based Illumina TruSight Myeloid Panel. I've compare…
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Using NerConverter in some situations produces an exception:
java.lang.StringIndexOutOfBoundsException: String index out of range: -1
## Description
In a pipeline wirh nerconverter and with s…
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Currently, when selecting a sequencer that has more than one lane (and thus accepts more than one pool), nothing prevents the user from mixing amplicon pool(s) with shotgun (plate) pool(s). Unfortuna…
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We would like to discuss how best to correct richness/alpha diversity for differences in sequencing depth (total amplicons) when using the default dada2 pipeline, i.e. when using dada(, pooled = FALSE…
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While Labman currently includes code to generate a Preparation Sheet (aka prep info file) for shotgun runs, those files do not follow the specifications required by Gail, who currently prepares the ma…
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Hello
I am trying to run the CRISPRessoPooled command on the pooled deep sequencing data.
i run my script several times as per suggestion, but got an error "ERROR: Flash failed to run, please check…
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I am having trouble getting nanopolish to work with amplicon data i have. I am attempting to create a consensus sequence with nanopolish variants. I tried with and with out --consensus option and rece…
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I'm trying to run the dada command to apply the sample inference algorithm to dereplicated data for my 16S samples. It fails for my dadaFs, saying it cannot allocate vector of a different size each ti…