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Popular Question to
JC
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Commentator to
Michael Dondrup
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Student to
MutationalMeltdown
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130
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Robert Sicko
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Recent Replies
Comment: Bioinformatics definition of TAD boundary
by
kalavattam
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50
> Can anyone provide a formal definition of TAD boundaries in bioinformatic language?
There's not a consensus definition of TAD boundaries…
Comment: Transcript enrichment in Illumina RNAseq
by
compuTE
▴
60
Thank you @friederike I'll check it out!
Comment: Bam file metrics
by
Ram
32k
Is it (samtools stat) fast though? I recall samtools being really slow compared to sambamba.
Answer: Bam file metrics
by
heskett
▴
10
Samtools stats is a new option for this. samtools is very reliable and easy to use in my experience
Comment: Single cell RNA-seq: how many PCs to use for t-SNE/UMAP?
by
MutationalMeltdown
▴
130
It depends, checks are essential but it can become too subjective if you're tweaking parameters to find 'what you want'- I also need standa…
Comment: ICE normalization using JuicerTools
by
kalavattam
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50
I might be mistaken, but I think 'bias' and 'weight' are synonyms in cooler/cooltools, e.g., [link][1]
[1]: https://github.com/open2c/c…
Comment: Single cell RNA-seq: how many PCs to use for t-SNE/UMAP?
by
MutationalMeltdown
▴
130
Thanks, I have used autocoders this way (was introduced by [this tutorial][1]). However, I've never actually found an autoencoder viz that …
Comment: design matrix considering treatment, timepoints and batches
by
Iván
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50
Anyone willing to input on this? Thank you! :-)
Answer: How to extend ChIP-seq reads from BAM file ?
by
heskett
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10
Bedtools slop can add bases in both or either directions to a read. very easy to use
Comment: XGBoost on the unbalanced data
by
Mensur Dlakic
★
10k
> The task sounds like pretty balanced
When one has 51:49 ratio of classes, or 55:45, or even 60:40, we can call that pretty balanced. A 1…
Answer: quick way to get samples that are NOT homozygous reference for a given record us
by
Pierre Lindenbaum
135k
bcftools view -i 'count(GT=="RR")==0'
Comment: How to combine 2 incomplete GTF
by
Juke34
★
5.4k
Could you show few lines of the original file? You will probably need to create proper gene feature first using an appropriate attribute (u…
Comment: Single cell RNA-seq: how many PCs to use for t-SNE/UMAP?
by
Mensur Dlakic
★
10k
I am not necessarily recommending autoencoders for visualization over t-SNE/UMAP either. In fact, I said above `it may not work for all dat…
Answer: Whole genome species clustering
by
h.mon
32k
I don't think there is a "best" approach in your situation, given
1) the taxonomy of the group is probably still flaky.
2) being dra…
Comment: Plink: Number of Samples reducing after merging multiple bed,bim,fam files with
by
Swetaleena
•
0
Also when I run this command in the folder having all my 34 separate .fam files, I get 2957. That means my merged.fam doesnt have the infor…
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