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Recent Replies
Comment: Checking sex of a sample with sequencing data
by
xqyn
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Yes, I have checked the signal on chrY data. The problem is that the sample have the peak signals for chrY in ATAC-seq data; however, it al…
Answer: Question about `vg construct`
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GBWT construction from a VCF expects that the paths representing variants are named by the hash of the variant rather than its identifier. …
Comment: FastQC on nanopore data: high proportion of polyA and polyG. Why ?
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GenoMax
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Have you considered contacting PacBio support? If they have any specific explanations please come back to this thread to add them here.
Comment: FastQC on nanopore data: high proportion of polyA and polyG. Why ?
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vkaz
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Yes, I am referring to PacBio HiFi data (even though original question was about nanopore data)
Comment: Alternatives to UCSC genome browser for obtaining gene coordinates
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Thank you for the reference, I'll look into it.
Incidentally, among other issues, UCSC Table browser feature seems to be buggy - for about…
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very strange. Can you please , upload the file below in a new issue : https://github.com/lindenb/jvarkit/issues
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samtools view -h in.b…
Comment: FastQC on nanopore data: high proportion of polyA and polyG. Why ?
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Original question was about nanopore data. Are you referring to PacBio HiFi data?
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If your peaks are in `narrowPeak` format, it may help to set the `PeakCaller` to `"narrow"`.
Comment: FastQC on nanopore data: high proportion of polyA and polyG. Why ?
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@Matt -- Hi, did you figure out about the cause of poly-A spike in your reads? I have similar problem in genomic HiFi reads.
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Okay so I used the command which you mentioned earlier, since I only want the reads which have a G to T substitution, I parsed the output s…
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Hi Istvan!
This was exactly what I was looking for! Amazing how 11 years after, this post is still usefull and active :)
I have a que…
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> The problem is that they all have many contigs (over 300)
That may indicate that these may not be "complete/reference" quality. How many…
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Genome assembly is still a trial and error process, but getting 39 million genomes for a 34-million-long expectation is not too bad.
Oft…
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Because it is a very common species and there are 15 available genomes around the size i mentioned. The problem is that they all have many …
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