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Recent Replies
Comment: Removing duplicates
by
quentinperriere
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thank you for responding.
I was looking for suitable variant calling tool. I'm working on fungus and I don't have fast5 files.
Could you re…
Comment: How to reduce the variation of CIBERSORTx results?
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Hi LChart,
Thanks for your reply. I see S-mode in the CIBERSORTx official website tutorial(https://cibersortx.stanford.edu/), and the imag…
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First time I've heard of S-mode. I imagine you've seen this benchmark where it doesn't come out too well: https://academic.oup.com/bib/arti…
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https://res.saletool.cn/vcf/18084521725806
Comment: ISCN annotation for SV/CN VCF files
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adedare
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https://res.saletool.cn/vcf/18084435127462
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I want to conduct GWAS meta-analysis using metal software.
Comment: How to reduce the variation of CIBERSORTx results?
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Hi LChart,
Thanks for your reply. Yes, the identical command lines produce different results in CIBERSORTx S-mode. Although I input the da…
Comment: Removing duplicates
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I *could* imagine an ONT scenario where you'd want to remove duplicates (amplicon-seq, etc) but likely for variant calling there is no need…
Comment: Removing duplicates
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As above, you do not need to worry about duplicates for ONT data
Also have you looked at using other tools for variant calling more suited…
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If you're looking for the GO annotations for *Pediococcus acidilactici*, these are available.
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I just found an answer to this question here:
[https://groups.google.com/g/cbioportal/c/hm_i4jbG1uc/m/h9rNYOvpAAAJ][1]
[1]: https://gro…
Comment: Removing duplicates
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With ONT you will only have PCR duplicates. 'Read' (you mean optical?) duplicates are an artifact of cluster-based sequencing (ie Illumina)…
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PacBio has some recommendations on software for genome assemblies on this page (which you may have seen but just in case): https://www.pacb…
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I would not put totally different tissues in the same DESeq object. I don't think that's going to do good things for normalization or disp…
Comment: Removing duplicates
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pcr duplicates or/and read duplicates
should I use this command to remove them ? or we don't talk about duplicates when dealing with ONT ??…
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