Most active questions
25 questions from the last 30 days
1
vote
1
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126
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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:
...
4
votes
0
answers
43
views
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
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
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 ...
- 65
1
vote
2
answers
18
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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 ...
- 11
0
votes
0
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28
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Choosing between Intel and AMD for bioinformatics and molecular dynamics workflows on Linux
I’m in the process of building a workstation for scientific computing, primarily focused on bioinformatics and molecular dynamics simulations. My daily tasks include:
• Genome assembly and ...
3
votes
1
answer
31
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Construction of 1000 genome phase 3 reference panel
Currently I'm learning to merge reference panel with WGS data to attain a more population-specific panel for imputation of SNP array data.
But I face 1 issue, it is not clear how to construct ...
- 31
2
votes
1
answer
19
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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
32
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STACKS process_radtags for demultiplexing RAD-seq data returning 57.5% "barcode not found" drops, retaining only 41.2% of reads
I'm having a very specific issue with demultiplexing my single-digest RAD-seq data using STACKS process_radtags. I have 389 individuals across 5 different libraries,...
- 11
-1
votes
0
answers
19
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How to respond the comment on the sample size in qPCR
In my bioinformatics article, I discuss the identification of MEG3 and MAPK3 as potential therapeutic targets for osteoarthritis prognosis. In the experimental stage, Tissue samples from three case ...
- 1
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 ...
- 1
0
votes
0
answers
20
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Warning in bcftools when subsetting a VCF by variant ID
I have successfully subset a VCF by variant ID after phasing and imputing using Beagle 5.5, however, I am getting the warning "[W::vcf_parse_info] INFO 'END' is not defined in the header, ...
- 1
3
votes
1
answer
15
views
Getting organism information from the ENA API
I have been generating Snakemake sample tables from a GEO identifier (GSExxxxxx) directly by making requests to the NCBI and ENA APIs. It works, but with some caveats (explained in this open question: ...
- 767
0
votes
1
answer
19
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Combining SCTransform, FindIntegrationAnchors, and Harmony
I'm trying to integrate 9 scRNA datasets from different publications. When using SCTranform combined with IntegrateData using anchors, the resulting UMAP is fairly noisy with some clear batch effect. ...
1
vote
0
answers
14
views
Unable to install cytoscape on the new version of sequoia (15.4.1)
I get this error message when trying to open the installer:
You can’t open the application “Cytoscape Installer” because this application is not supported on this Mac.
I am pretty sure this is ...
- 11