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Comment: Get protein information from ensemblbacteria using interpro
by
sgiorgetti
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10
@GenoMax Apologies for my belated reply.
Agreed, the REST endpoint above supports Ensembl IDs only. Mentioned because both the initial que…
Comment: VEP tab/vcf - Different output
by
Ben_Ensembl
★
2.2k
Ah, I see. Then, no, I don't believe that this is possible with the VEP
Comment: VEP tab/vcf - Different output
by
Jeremy Leipzig
21k
I don't think that is in VCF-style coordinates which show deletions like chr1:99:AG -> A instead of chr1:100:G -> -
Comment: Help with running ATAC using Encode pipeline
by
Chris
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Sure, here is my json file, I have 8 fastq files:
{
"atac.title" : “atac)”,
"atac.description" : “Encode”,
…
Comment: Differential protein expression analysis
by
dsull
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4.2k
Yes, you need to log-transform.
I've had a good experience using limma for proteomics analyses (limma uses a moderated t-test).
Answer: Assigned taxonomy after dada2 only "NAs" or "Mitochondria"
by
mattze731
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Never mind. Someone had put all the 16S files into the ITS folder and vice versa. After using the 16S dada2 pipeline on the actual 16S file…
Comment: Getting Pairwise Sequence Alignment Score With Biopython
by
Jonathan Lefebre
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Dear Alexander,
to answer 2) first: This is just a fasta file that you can obtain essentially from every multiple sequence alignment soft…
Comment: Stratified sample assignment for analysis
by
ATpoint
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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
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colindaven
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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
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i.sudbery
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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
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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
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Alexander
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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
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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…
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