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Recent Replies
Comment: Removing duplicates
by
joe
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490
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
by
samuel.a.odonnell
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510
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…
Answer: Pediococcus acidilactici sequence analysis
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geneontologyhelp
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If you're looking for the GO annotations for *Pediococcus acidilactici*, these are available.
Using the instructions under [*2. All other…
Answer: What is the normalization status of metabric data?
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etiennedanis
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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
by
joe
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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)…
Comment: assembly using CCS, CLR, CCS_CLR sequences together?
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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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quentinperriere
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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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If you didn't change the input signature matrix, the input RNA matrix, or the input parameters - what did you change? Is the statement that…
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> To replicate GVCF behavior and avoid issues with 0/0 genotypes appearing as missing, I don't use the -v option
I'm not sure what you m…
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Your best option may be to email the author (and/or the senior author from the paper). Let them know that the FTP links mentioned on GitHub…
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Thanks @lchart, I accept that, I'll wait to see if there's any more who want to input and then accept the answer
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What kind of data is this? Plain genomic/amplicons? How you proceed will largely depend on the context. Can you also post the original fast…
Comment: Removing duplicates
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I guess the enlightening question is: duplicates of what?
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I don't think this approach will give you what you want. Combining multiple tissues in the way you are suggesting will result in a positive…
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