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You can specify the number of mismatches for `addSpacerAlignments` using `n_mismatches` and you can do the same for `addOffTargetScores` using `max_mm`. Should there ever be a difference between the v…
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I'm trying to use STAR to align RNA-seq data to a bacterial genome. Because the annotations were generated with Prokka (https://github.com/tseemann/prokka), there are no exons per say. Maybe the clo…
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Hello,
I used Nanoraw before and with Nanoraw the table Events must be present in Analyses/Basecall_1D_000/BaseCalled_template/, right ? I found that logical.
With tombo, it's no necessary. It see…
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**1. What were you trying to do?**
I was trying to create a gsca index of a graph created with pggb.
**2. What did you want to happen?**
The index to be created successfully (as happened…
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Hi, the samtools flagstat does not seem to work for me. I get the following error, the 'quickcheck' gives a good report. Does anyone point me to what might have gone wrong.
```
$ samtools flagstat F…
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Hello! Really great tool. For me, the hive plot function appears to be very useful. But I encountered with an issue when aligned sequences as you have described in your decumentation. I did it this wa…
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Hi @GMOD team,
The fields of epigenetics and now epitranscriptomics have evolved very fast in recent years and there are now a few DNA and RNA modifications which can be detected at single molecule…
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Hi,
I am excited to be using the new gatk4 workflow on a fresh bcbio development install. In this case I'm running a tumor/normal pair of targeted DNA-Seq from pre-aligned bam files. I've read mixe…
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I used Arioc to map reads to my reference genome twice but both sam files has erroneous characters generated and it cause samtools view to abort with error `[W::sam_read1] Parse error at line 2602870`…
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Hello Maria,
We are trying to use Ribbons for data analysis of viral integrations into the human genome sequence. Unfortunately, we have encountered an issue with one step of the analysis. Specifi…