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There is an odd behaviour we encountered for EMA aligning against the hg38 reference genome. For some reason many reads appear to map to the N stretch in a beginning of a chromosome. Below is an IGV s…
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Related to #413 . This one is more specific for Longranger (version >= 2.2) and writing a module for the WGS sub-pipeline. I will also take a look at the exome ("targeted") pipeline, but I am missing …
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Dear ARKS team,
looking forward to testing your tool, but got stuck right away with the required input format.
Specifically, how are these interleaved files generated? Our Chromium output consi…
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I'm new to linux and kubernetes so this might be something I'm doing wrong rather than a bug.
Installing seqr on Ubuntu 18.04.1, VM=VirtualBox. All goes fine until deploying seqr pod, then throws fir…
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Hi,
I'm trying to run Valor for inversion detection. I was able to complete a test run successfully on a sample BAM file on our local compute cluster. However, when I try to run in a docker contain…
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As far as I understand, you trim 16+7 based from the first read only, and leave the mate read alone:
> In summary, in the barcode extraction stage, we remove the 16bp barcode from the first mate
o…
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Hi
I had previously submitted an issue (#231), we have a large amount of data, almost 1TB, and our machine has about 512 GB of available memory, we used abyss in a command like this:
```
abyss…
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How is it possible to assemble only 10X data using abyss? (there isn't any paired-end or mate pair lib) and how if we have multiple libraries of 10X data?
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In the interleaved fq Examples/arks_test-demo/test_reads.fq.gz the read headers of mates have identical names:
```
zless Examples/arks_test-demo/test_reads.fq.gz | head -n 8
@gi|453232067|ref|NC_…
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Hi Thomas,
I'm trying to use .bams from 10x genomics with HipSTR. It looks like all reads are getting filtered out. for example when I run against your precompiled .bed file all the entries look like…