User: Carambakaracho
Carambakaracho • 1.2k
- Reputation:
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- Switzerland/Basel
- Last seen:
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- Joined:
- 3 years, 6 months ago
- Email:
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Bioinformatics and application specialist at a midsize bioinformatics company, Basel
Posts by Carambakaracho
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Comment:
C: Convert fasta headers to GFF
... Thank you both. I know the GFF3 flexibility is a nightmare. Especially because too many people don't seem to care much about the (very) long specs.
Part of my job is integration of genomes and their annotation into structured databases, and from that perspective GTF isn't any better (for example r ...
written 7 days ago by
Carambakaracho • 1.2k
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Comment:
C: Convert fasta headers to GFF
... Hi [@Devon][1], my apology for hijacking this thread. I'd tend to disagree with your opinion on GTF vs. GFF. While I have no particular affection for GFF, at least it comes with [comprehensive format specifications][2] - which I haven't seen for GTF, yet. Of course specs are only as good as their im ...
written 7 days ago by
Carambakaracho • 1.2k
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... - Can you print the address you send and try via your browser?
- Is it an http address (not https)? (though unlikely as you wrote it worked weeks ago)
...
written 11 days ago by
Carambakaracho • 1.2k
2
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100
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Comment:
C: SPADES contig output
... no, not as far as I know.
SPAdes uses bwa to align the reads back, so you'll have to go that way, too. There used to be a bwa binary with distributed spades ...
written 11 days ago by
Carambakaracho • 1.2k
0
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... HI Ankit, i'm not a specialist on methylation data (not even a bit).
Do you really think a simple test is what you want? I mean, you obviously have a difference between patient and control and not so much if any between parents and control. Would it be more interesting to figure where there's diff ...
written 12 days ago by
Carambakaracho • 1.2k
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... > Are there any plots or values which I need to show here?
in case you want someone to give qualified answers, that might help. How about the violin plots and box plots you mentioned? With box plots histograms are helpful, too (though included in the violin plots). ...
written 14 days ago by
Carambakaracho • 1.2k
0
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... > Does my data full-fill the assumptions as mentioned here?
You don't show the plots you produced. What Jean-Karime wrote above still holds true.
>That can't be decided without knowing the data.
...
written 14 days ago by
Carambakaracho • 1.2k
0
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1
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146
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... To me a violin plot is mostly a fancy representation of a box-plot. And a box plot is (for gaussian distributions) a graphical representation of a t-test. ...
written 14 days ago by
Carambakaracho • 1.2k
2
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1
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99
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Answer:
A: Clustal Omega and Biopython
... This one is fairly simple I guess. The way you wrote it, Python has to interpret `phylip` as a variable. You never assigned any value to this variable when you use it the first time. Either you declare it as string, or assign the string phylip to a variable beforehand.l
clustalomega_cline = Clu ...
written 20 days ago by
Carambakaracho • 1.2k
2
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153
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... I can't add much to what hmon commented besides some own experience :
I tried years ago something similar and failed. What convinced me at that time was aligning the assemblies and I wasted quite some days until I reached the conclusion.
At that time I learned that the N50 alone is a poor quality ...
written 25 days ago by
Carambakaracho • 1.2k
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For A: Calculate CDS phase in gff3 format
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