Moderator: b.nota

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b.nota5.0k
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Posts by b.nota

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Comment: C: What exact statistical method should I use to compare coverage profiles of two s
... Decide for yourself the threshold of *depth of coverage* for each amplicon. If a sample contains an amplicon with less than that *depth of coverage* "something is wrong" I would say. Maybe make a barplot of each new sample, each amplicon a bar with the *depth of coverage*. Just an idea. ...
written 1 day ago by b.nota5.0k
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Comment: C: What exact statistical method should I use to compare coverage profiles of two s
... But why do you use targeted seq? For mutation analysis or just to see how many amplicons you get? If you have designed this panel for mutation analysis, your validation should be that you can find the mutation in both samples. ...
written 1 day ago by b.nota5.0k
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Comment: C: What exact statistical method should I use to compare coverage profiles of two s
... What is the goal of your experiment? You must have a plan before you start sequencing. Usually targeted sequencing is to find mutations. ...
written 1 day ago by b.nota5.0k
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Answer: A: Sequenced sample twice, can I merge the fastqs to analyze?
... In my opinion this does not seem like a good idea. If your quality is bad, don't use it. If you really would like to use technical replicates in your RNA-seq design (and ignore the fact that you have bad quality), you can use the `duplicateCorrelation` function in `limma` to include the technical re ...
written 2 days ago by b.nota5.0k
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Answer: C: how to compare proteomics data?
... If your data is properly normalized, you can try limma. I have been using limma for LFQ normalized ms/ms data. Of course you need biological replicates (if you have them it is not clear from your post). ...
written 2 days ago by b.nota5.0k
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Comment: C: summary statistics on fasta sequence for ABC
... Forums are more meant for opinions and sorts. ...
written 2 days ago by b.nota5.0k
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Comment: C: IonTorrent variant calling: "Missing ZM: tags"
... Did you call Thermofisher for support? It is commercial software right? They can at least give support for the money they got from you. ...
written 12 days ago by b.nota5.0k
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Comment: C: Must I feel useless or not?
... Sounds like you would benefit from talking to a career coach or counselor or something. If you want to continue in bioinformatics, because your heart is there, try to become better at it (learn how to write programs, learn about statistics). But if your passion is not bioinformatics, please consider ...
written 13 days ago by b.nota5.0k
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Answer: A: extracting first exon and corresponding transcript coordinates
... You can use biomaRt, [here][1] a previous post for metazoan exons. But for human it is also possible. Try the biomaRt manual to figure it out yourself first. If it doesn't work, please add some code of what you have tried. [1]: https://www.biostars.org/p/319403/#319404 ...
written 14 days ago by b.nota5.0k
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Comment: C: fastq file do not look as they should (running Hisat2)
... Haha, do you want me to remove my answer? ...
written 15 days ago by b.nota5.0k

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