User: Macspider
Macspider • 3.0k
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Posts by Macspider
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... True. Thanks for the point of view! ...
written 13 days ago by
Macspider • 3.0k
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... We do have ample sample and we have enough budget. The most crucial part is to choose a path that returns sufficient results because a person in the project has limited time to complete their part of the analysis :) ...
written 13 days ago by
Macspider • 3.0k
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... Hi everyone,
I am exploring the possibilities I have for an RNA meta-transcriptomic sequencing experiment involving Nanopore. Disclaimer #1: I'm a bioinformatician, so I don't have much wet lab background to choose a couple of things in my workflow. Disclaimer #2: I will post this also on the Nano ...
written 13 days ago by
Macspider • 3.0k
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... The same way you would except any other error in python, nothing fancy. ...
written 4 weeks ago by
Macspider • 3.0k
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... Yes, please read through this github issue that I closed some weeks ago, I believe it's the same issue :)
https://github.com/MatteoSchiavinato/Utilities/issues/1
(to improve readability, could you wrap the code parts of your answer inside a code block?) ...
written 8 weeks ago by
Macspider • 3.0k
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... Yes, I am afraid so. If this information is not stored during the pileup, it won't be possible to extract it from a VCF file. ...
written 9 months ago by
Macspider • 3.0k
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... When you do the pileup, for example with samtools, you can require additional tags to be present in your `INFO` and `GENOTYPE`. These are specified via the `-t` option. I usually ask for:
−t DP,AD,ADF,ADR,DP4
Note that DP4 is deprecated but still present in the output if you require it. It con ...
written 9 months ago by
Macspider • 3.0k
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... Have as much as you need within programs that you can re-run at any time, save all logs possible. This is really 90% of the efficiency, imho! Everytime something like this happens, you be like changing your script parameters and re-run it. Even if it took a lot to get where you are, re-running it wo ...
written 9 months ago by
Macspider • 3.0k
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... I work routinely with FASTQ files that are > 500GB and I would repeat the whole analysis ^^ putting every command into a script doesn't take so long, after all, if they execute one after the other. ...
written 9 months ago by
Macspider • 3.0k
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... This might be the best suggestion you'll ever receive about it. ...
written 9 months ago by
Macspider • 3.0k
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