User: Macspider
Macspider • 3.0k
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Posts by Macspider
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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 4 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 4 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 4 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 4 months ago by
Macspider • 3.0k
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... This might be the best suggestion you'll ever receive about it. ...
written 4 months ago by
Macspider • 3.0k
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... This is a very "philosophical" question, but to cut it short, many people in the past have used a minimum threshold of FPKM >= 1. This value is extremely eye-metric and not based on robust statistics.
It will, however, eliminate a lot of noise, and it will be easy to reference why you chose tha ...
written 4 months ago by
Macspider • 3.0k
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... On the same train of thought as @genomax, I would say that also brackets, pipes and equals could be avoided. Not because they could damage you *now*, but because you'll never know what you'll need these data for in the future. Those characters could easily mess up your future pipelines!
Something ...
written 4 months ago by
Macspider • 3.0k
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... I edited the command in my first comment. It now has a start `*` after the numeric specification `[0-9]`. This means that any *sequence of numbers* from 0-9 will now be deleted. ...
written 4 months ago by
Macspider • 3.0k
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... cat $filename | sed 's/>.*cds_/>/' | sed -e 's/_[0-9]* \[/ \[/'
*First sed*
Each character (.*) that is contained between `>` and `cds_` is replaced by only `>`. This leaves the FASTA header intact but removes everything until `NP_`.
*Second sed*
Enabling regular expressions (` ...
written 4 months ago by
Macspider • 3.0k
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... The community is generally more used to FPKM but the author of FPKM itself said that we should move on because it is biased ([ref][1]).
Also, you can convert FPKM to TPM using [a formula][2]. And if you can't access that formula, I also report it in [one of my papers][3] (see methods section "ΔXT/F ...
written 4 months ago by
Macspider • 3.0k
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