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Comment: How to assess differential gene expression over gradient of treatment levels wit
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CephBirk
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In this setup, how will DESeq2 handle genes that may not be very differentially expressed between low and intermediate factor levels but th…
Comment: Viral load / Relative viral load estimation from NGS data – is it possible?viral
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GenoMax
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> So far, the kit seems to only support reporting pathogen presence/absence.
There may be a reason for that. Did you take a look at the me…
Comment: Integrity of bam files
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SHN
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40
Thank you for your information, I'll follow along and make justifications in my code.
Answer: primer
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GenoMax
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While you can use command line tools you may find it easy to simply use this web front end: https://primer3.ut.ee/ , https://www.primer3plu…
Comment: Integrity of bam files
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GenoMax
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While the read numbers seem to match, I would be weary of using data where the analysis step did not complete normally.
Comment: is there publicly available tool for assembly of bionano data
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Aleksandra
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Unfortunately, no, this link is not to the tool I was talking about, but I think the only thing I can confidently recommend is the official…
Comment: Uninformative Cluster in scRNAseq
by
Arup Ghosh
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I would recommend performing an additional filtering step for cells with a high quantity of haemoglobin genes.
Comment: Splitting VCF using phase information
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cmdcolin
★
4.3k
variants that use a slash (/) are actually unphased. if they have a vertical bar (|) then they are phased. disclaimer: I made this, but we…
Comment: is there publicly available tool for assembly of bionano data
by
GenoMax
153k
No need to apologize. You are trying to help people, which is great. My comment was mainly to improve your post.
In comment above you ment…
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Aleksandra
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Excellent follow-up questions.
Regarding your first point, you should definitively perform the PCA on the post-imputation dataset. Because …
Comment: is there publicly available tool for assembly of bionano data
by
Aleksandra
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There is no single assemble command in OMTools. It is not a monolithic program, but a set of separate scripts that must be executed sequent…
Comment: is there publicly available tool for assembly of bionano data
by
Aleksandra
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100
My recommendation regarding OMTools was based specifically on comment about working with older data, as it was a stable academic standard f…
Comment: is there publicly available tool for assembly of bionano data
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eebloom
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I cant see a command on OMToolsManual.pdf which says it takes .bnx.gz files and assembles them in to contigs (.cmap)
Comment: Integrity of bam files
by
SHN
▴
40
Thanks for your response. I performed alignment summary
47714869 reads; of these:\
47714869 (100.00%) were paired; of these:\
…
Comment: How to troubleshoot strange hyperparameter trace from BSLMM (GEMMA)
by
gina.maria
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Thank you very much for the answer, this is very helpful! Regarding the PCA I have a couple questions:
I used BEAGLE to perform imputatio…
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