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Popular Question to
JC
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Michael Dondrup
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MutationalMeltdown
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Robert Sicko
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jared.andrews07
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Recent Replies
Comment: design matrix considering treatment, timepoints and batches
by
Iván
▴
50
Anyone willing to input on this? Thank you! :-)
Answer: How to extend ChIP-seq reads from BAM file ?
by
heskett
▴
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…
Comment: Plink: Number of Samples reducing after merging multiple bed,bim,fam files with
by
Swetaleena
•
0
When I run this command for my merged.fam file, I get 2480. But originally, I had 34 bed,bim and fam files for 3061 samples which I merged …
Answer: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover,
by
bw.
▴
180
I recently put up https://liftover.broadinstitute.org/ to make it a little easier to check liftover coords for specific variants or interva…
Answer: Alternatives To Liftover
by
bw.
▴
180
I recently put up https://liftover.broadinstitute.org/ to make it a little easier to check liftover coords for specific variants or interva…
Comment: Plink: Number of Samples reducing after merging multiple bed,bim,fam files with
by
Lemire
▴
600
You might have duplicated IDs in your file*.fam?
How many unique lines do you get when you run
cat file*.fam | awk '{print $1,$2}' …
Comment: error in compare.py of CNCI package
by
IA
•
0
(2.7 years later) Did you find the answer to this problem?
Answer: Simple Progress Bar with Alignment
by
dariober
12k
Not a definitive answer but...
> missing dependencies which I have to manually install and which may not be compatible with the R version …
Comment: single cell RNA QC
by
leranwangcs
▴
40
Thanks so much @jared.andrews07! This is the information I need!
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