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Recent Replies
Comment: Bioinformatics: what do you think of it in the next 20 years?
by
GenoMax
136k
> what do you think of it in the next 20 years?
It will be what people like you make of it (assuming you are just starting out and that is…
Comment: Fastest way to convert BED to GTF/GFF with gene_ids?
by
cmdcolin
★
3.4k
thanks for making these great tools
Answer: Dimensionality reduction on data sets with variable dimensions
by
Mensur Dlakic
★
25k
Not sure whether what you want to do will be informative. That aside, UMAP works with sparse data. Simply insert missing values for shorter…
Comment: best BLAST hits - which criteria is more important?
by
Mensur Dlakic
★
25k
If your goal is to find the most similar sequence to your references, you have a correct sorting order. The next two criteria should probab…
Comment: best BLAST hits - which criteria is more important?
by
min
•
0
thank you for correcting me. What I actually did was run a search using mmseqs2 and diamond to find similar enzymes in a MAG for my referen…
Answer: Fastest way to convert BED to GTF/GFF with gene_ids?
by
alejandrogzi
▴
100
This is probably a duplicated question from:
[How To Convert Bed Format To Gtf?](https://www.biostars.org/p/64346/)
[How to convert …
Comment: From TPM to raw counts
by
Gama313
▴
120
I will give it a try and I will report results! Thanks for your help!
Comment: Bioinformatics: what do you think of it in the next 20 years?
by
Mensur Dlakic
★
25k
Complaining about format conversions is like a wet biologist complaining about Westerns to prove protein expression. It is tedious and has …
Answer: best BLAST hits - which criteria is more important?
by
Mensur Dlakic
★
25k
There is no way to run BLAST using mmseqs2 and diamond. Maybe you mean that you compared sequences using mmseqs2 and diamond?
> I need to …
Comment: Bioinformatics: what do you think of it in the next 20 years?
by
Istvan Albert
99k
10 years ago https://www.biostars.org/u/36/ told us:
>I've been doing bioinformatics for about 10 years now. I used to joke with a friend …
Comment: From TPM to raw counts
by
Istvan Albert
99k
Now that I thought about it more, you'll need the total number of reads mapped to produce the normalization factor.
You can undo the TPM o…
Comment: How Can I move the scattered dots more closer into the center of box ?
by
ohtang7
▴
40
You're right. I would get help from StackExchange sites and GPT
Answer: Is bisulfite-seq data from different studies comparable with each other?
by
NextGenSeek
•
0
The efficiency of bisulfite treatment itself can differ significantly, so I would definitely not compare bisulfite-seq data from different …
Comment: Issue with genetic QC sex check
by
kl
▴
10
After setting set-hh-missing, I have the following boxplot, where a F statistic of 0.91 corresponds to a female in my phenotypic dataset wh…
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