Newest Questions
6,549 questions
2
votes
1
answer
19
views
What tool to use for visualizing combined TF binding sites and H3K27me3 enrichment across multiple cell lines using deepTools?
I'm analyzing ChIP-seq data for the transcription factor of interest (TF) and the H3K27me3 histone modification across three different cell lines: H9, HSMM, and iPSC. For each cell line, I have:
TF ...
1
vote
0
answers
36
views
CRISPR Screen Alignments Mystery
I am analyzing a CRISPR screen. Illumina MiSeq, 5 million 75PE reads, and a PhiX spike in of 10%. The experiment is a depletion CRISPR library over time of a cell line.
It is a subset of 700 guide ...
1
vote
2
answers
18
views
Will Cytoscape allow me to draw a network piece by piece and test claimed interactions?
As a scientific editor, I sometimes need to envisage proposed gene–enzyme–metabolite networks while editing papers. Being a visual thinker, I have to plot the claimed interactions and effects (as ...
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2
votes
0
answers
25
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What is the difference between JASPAR IDs MA0668.3 and MA1993.2 for Neurod2?
I was looking into the JASPAR database for transcription factor binding motifs related to Neurod2, and I found two ids:
MA0668.3
MA1993.2
Both IDs correspond to the same transcription factor (...
- 21
4
votes
0
answers
43
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Understanding NCBI eutils API results
I have made a Python function that can turn an NCBI GEO identifier (GSExxxxxx) into an ENA bioproject accession using the NCBI API. I need this to get sample tables which I then feed into Snakemake. ...
- 767
0
votes
0
answers
20
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Cytoscape stringapp takes too much time getting protein queries and cloudflare's servers time out
I'm trying to load a list of 19153 genes in Cytoscape with the stringapp protein query, but since the list is gigantic, it takes a lot of time to gather all the protein names and cloudflare's server ...
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1
vote
0
answers
12
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Automated Molecular Docking Script for Library of Receptor Proteins and Singular Ligand
My experiment is to see if a lipid molecule binds to the surface proteins of a class of cells, to see if there is potentially an interaction.
I am relatively new to molecular docking, but am curious ...
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0
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0
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9
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Inquiry about using EMBOSS MATCHER with Python
I am new to Bioinformatics and want to know if this is possible. I have a .txt file with a series of 50 gene sequences and I want to know if I can find the identity of them iteratively through a ...
1
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0
answers
45
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Add statistical test to this ggplot boxplot in R
Good morning,
I was wondering if anyone could assist me with the following: I am struggling to add a statistical test to this boxplot like a bar (preferably with Wilcox test). I tried with adding ...
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1
vote
1
answer
126
views
How to subset a large BAM file using BED file?
I have few NIST BAM files which require to be filtered for reads that are overlapping regions with the BED file. I have tried the following command using samtools:
...
2
votes
1
answer
23
views
Weighted mean allele frequency (x-chromosome) calculation
This is a well-known formula that I found in a printed book:
$AF = \frac{(AF_{female} \hspace{4mm} \times 2 \times N_{females} \hspace{4mm})~+~(AF_{male} \hspace{4mm} \times N_{males} \hspace{4mm})}{2 ...
- 131
2
votes
0
answers
12
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BEAST Low Posterior ESS and Posterior Support Values for MCC nodes
I've been working with BEAST for the past couple weeks to try to make a comprehensive phylogeny of 16S for a genus of frogs. There are two groups of interest to me: the mainland clade and the ...
2
votes
1
answer
8
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PSIMI 25 style has disappeared from Style menu in Cytoscape [Cytoscape]
I have used the PSIMI 25 style, which was a built-in style, to be able to easily distinguish human proteins/nodes from non-human ones in Cytoscape (I'm using 3.10.3) networks. This seems to have ...
3
votes
1
answer
37
views
analysis of a few genes in RNA-Seq datasets
I'm analyzing the gene expression of three genes in several RNA-Seq datasets (each dataset investigates a different disease - I'm evaluating the difference of RNA counts in healthy vs disease).
I'm ...
- 119
2
votes
0
answers
16
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How to match output alleles of modkit and sniffles2 outputs in the wf human variation pipeline?
I am using the wf-human-variation pipeline to obtain (1) DNA methylation data and (2) structural variation data. According to their documentation, the methylation results are labelled according to ...
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