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Recent Replies
Comment: PCA plots in ATAC-seq replicates: Is it okay to use vst transformed data for vis
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ATpoint
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> but I know vst is usually for RNA-seq
It's just a transformation that unlocks the variance from the mean, you can use it here with no pr…
Comment: Checking sex of a sample with sequencing data
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xqyn
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can you give any thought? (scale:0-2000)
![ (can you give any thought?][1]
[1]: /media/images/fa316655-e25e-46a6-adf6-15a5db66
Comment: FastQC on nanopore data: high proportion of polyA and polyG. Why ?
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they recently released a version specific for long reads: [fastplong][1]
[1]: https://github.com/OpenGene/fastplong
Comment: Checking sex of a sample with sequencing data
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ATpoint
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So you mean you see peaks at Xist which makes you think it's activate X-inactivation, hence its female? Can you show some plots or anything?
Comment: Checking sex of a sample with sequencing data
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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…
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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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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.
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very strange. Can you please , upload the file below in a new issue : https://github.com/lindenb/jvarkit/issues
```
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?
Answer: DiffBind normalization error: invalid argument type (list) - cannot make it work
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Rory Stark
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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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vkaz
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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.
Comment: Find the reads which correspond to DP of vcf
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totoroGirl
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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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