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Recent Replies
Comment: Stratified sample assignment for analysis
by
ATpoint
72k
Batches for what? Processing/sequencing, what data are we talking about? If this is indeed paired then you basically must keep samples of a…
Answer: Visualizing Graph Alignment Format via minigraph
by
colindaven
4.8k
That's a really good question. Short version: not much to my knowledge, aside from looking at it, or filtering it (as it's a PAF like forma…
Comment: Alignment of case vs. control from different origin
by
i.sudbery
17k
BTW - Most TCGA cancer types do have normals amoungst the samples.
Comment: Alignment of case vs. control from different origin
by
i.sudbery
17k
The assumption of these studies is that any batch effect within a batch affects both treatment and control equally, so that when you divide…
Answer: Stratified sample assignment for analysis
by
Vincent Laufer
★
2.9k
First, you didn't tell us what kind of data you are working with. For arguments sake, I'll assume bulk RNA-seq.
Generally, your options …
Comment: VEP tab/vcf - Different output
by
Ben_Ensembl
★
2.2k
You can use the ---show_ref_allele flag when running the VEP query. This will add the reference allele in the output and is mainly useful f…
Comment: Get relationships and hierarchies for GO terms
by
Alexander
▴
70
For R-users might be interesting to look at notebook "CAFA5: train set GO terms" https://www.kaggle.com/code/antoninadolgorukova/cafa5-trai…
Comment: Getting Pairwise Sequence Alignment Score With Biopython
by
Alexander
▴
70
Thanks for sharing ! Just these days I am trying to wrap my mind on protein alignments.
I wonder: 1) "PID" in your post is "percentage o…
Answer: What kind of statistical test does Cellranger count use?
by
fracarb8
▴
950
You should read the [cellranger documentation][1] to understand how the analysis are performed. For example, it uses `graphclust` for clust…
Answer: Gene prediction software
by
alexandru.bologa.marian
▴
40
Hi,
I don't know if there are tools designed to predict pseudogenes, but If i understand correctly from your post you could predict all th…
Answer: Getting Pairwise Sequence Alignment Score With Biopython
by
Jonathan Lefebre
▴
60
Maybe quite late, but in case other people are looking for this. Pairwise sequence identity can be easily calculated using basic python fun…
Comment: Getting same value for start and end position, "DNA methylation"
by
ATpoint
72k
Yes, that is what methylkit is for. See my answer.
Comment: Italicise annotations with pheatmap
by
ATpoint
72k
Inkscape you learn in a day, for basic image and figure manipulation it's really simple and a good skill to have. Highly recommended.
Comment: Installation of PPFinder
by
subashini.fbtpb106
▴
10
Can you suggest me any software that does gene prediction by masking pseudogenes?
Comment: variant allelic fraction
by
Pierre Lindenbaum
154k
IMHO this is like asking for the cow when you only have a steak :-)
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