Recently Active Questions
6,549 questions
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Sanger sequencing annotation error
I am a student in a Cancer lab. Working with sanger is new to me. While analyzing a report we found an insertion that has not been reported in any databases so far, we were working on checking if the ...
CommunityBot
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1
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27
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Assessing Quality of Error Correction
The main idea:
Given fastq/fasta files containing reads(simulated from ref. genome, with errors introduced) and another file with the ground truth(simulated but without errors) and then the resulting ...
CommunityBot
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0
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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,...
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167
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How to remove third codon positions from a charset in iqtree?
I need to build a phylogenetic tree using IQ-TREE, starting from a sequence alignment in CODON format of several invertebrate mitochondrial genes. These are my charsets:
...
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0
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BioID SAINT downstream analysis
I have SAINT results which contain 2 types of baits CCER2-C and CCER2-N. I need to determine proteins which interact with CCER2-C vs CCER2-N. I have come across heat maps and dot plots by Prohits-viz ...
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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. ...
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1
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49
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What algorithm should I use to find what RNA sequence/structural elements lead to different labelled MFE values?
To put it super simply: I have RNA sequences, their optimal secondary structures, and the MFE values of those structures. I'm trying to computationally identity what structural elements and/or ...
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248
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Getting all promoters of a specific gene
I'd like to perform a motif analysis of all promoter regions of the gene ENSMUSG00000020538 in mus musculus.
To do so, I wanted to use Biomart :
...
CommunityBot
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67
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Arbovirus phylogenetic analysis using the BEAST2 software via a global clock model
How do I perform a global clock phylogenetic analysis of an arbovirus using the BEAST2 software. If I intend to utilize the global clock model for analysis, kindly guide how to set the parameters of ...
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2
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1
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557
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calculate mismatch frequency/rate from a BAM file
I am working with PAR-CLIP data where experimental procedure induces T to C mismatches. The other types of mismatches we can consider coming from artifact such as PCR errors. It could also be an ...
CommunityBot
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412
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Will using smaller kmers help get larger contigs? If not, then what?
I've been using MEGAHIT to assemble metagenomes, with particular focus on specific genomic areas.
Sometimes all I get is gene fragments or pathway fragments (eg. if I know that genes A, B, C, D and E ...
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2
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85
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Jalview interface issues
I have encountered few problems regarding Jalview after updating my OS to Windows 11:
whenever I try to open a sequence file, Jalview instead loads the
same MSA of sequences imported from UniProt, ...
CommunityBot
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3
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1
answer
15
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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: ...
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ChimeraX AlphaFold3 prediction pseudobond naming
I had a question about how to label the residues between which pseudobonds occur in ChimeraX 1.9.
I generated pseudobonds by using the PAE output from AlphaFold3 and the command
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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 ...
