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Hi there,
Have been using your library to demultiplex libraries - 384 well illumina libraries per ONT run - which have a similar construction to Tru-seq paired indexes.
The first sets tested w…
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I'm experiencing a weird thing when I use filterandtrim on some samples from a recent run, I haven't experienced it before, I've put two examples in here.
There are>100.000 reads for almost all sa…
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Hi,
If I called a heterozygous SNP with short read, then phase it with long-read.
But in long-read, at the same position is not a heterozygous SNP,
may be it is a homozygous SNP or no SNP.
What wi…
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Hi,
thanks for putting together a great resource for novices to genomics data analysis!
I would suggest changing the wording in the subsection "Align reads to reference genome". Currently it rea…
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Hi Folks,
I would like to know if the adapters are included in both ends of reads, due to the short insert (100 bp) during library construction. the Hiseq PE-150 was used for sequencing. How does t…
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One consequence of the recommended op-orders `CGQAW` and `GAWCQ` is that garbage reads may end up being trimmed to lengths of 0 or shorter than the provided window size in the `--overwrite-low-quality…
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Hello BWA-mem2 team. Would it be possible to handle unaligned BAM as input? This unaligned BAM file might have single- or paired-end and they would be processed simultaneously.
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https://doi.org/10.1101/092890
> Next-generation sequencing (NGS) is a rapidly evolving set of technologies that can be used to determine the sequence of an individual's genome by calling genetic v…
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Hi,
First,
I am wondering the step:
` Finally, the HiFi and short reads were combined to polish the ONT assembly. `
What software did you use to polish the genome?
Second,
what are the sequenc…
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Hello,
I have successfully run the superSTR software for the processing and postprocessing steps without error, but the motif screening step runs until 19% and then reports an error:
> "Attribut…