Bioinformatics Stack Exchange
Bioinformatics Stack Exchange

Most Popular

more tags
1500 questions
5
votes
1 answer

Are there certain alignment methods/tools which perform better with a high density of indels?

I have a set of experiments which should result in WGS reads with a high density of indels. Question: Are there certain alignment tools/methods which perform respectively "better" with these reads? I'm not very interested in performance, but rather…
EB2127
  • 1,413
  • 2
  • 10
  • 23
5
votes
1 answer

How are positions visually indicated in the UCSC Genome Browser?

I'm a little confused about how the position indices work in the browser. Based on the picture below, is base number 755440 an A or a G? The general question is how do the indexing guides work? Is the base right under the | the one corresponding to…
Paghillect
  • 309
  • 1
  • 7
5
votes
1 answer

Can I use DRIMseq to model interaction effect of variables?

I am trying to use DRIMseq for DTU with 2 treatments on two different strains of mice. In my previous analysis with genes only, I had found a strong interaction effect of strain and treatments. Is it possible to model that with DRIMseq? Also when…
Saumya Kumar
  • 51
  • 1
5
votes
1 answer

Evaluate clusters of individuals by using their sequence data

For a dataset of several hundred individuals, I applied a hierarchical clustering to generate clusters based on a functional trait that sets them apart. My task is now to evaluate if these clusters can be supported by the nucleotide sequence data…
Laaas
  • 51
  • 2
5
votes
0 answers

How to create a pathway knockout using the JavaScript library ESCHER?

I want to create my own pathway with a custom knockout function using ESCHER. Consider the pathway knockout link. As you can see by clicking the reaction the color changes and the text with the html/css id knockout-status adds the reactions that…
A.Dumas
  • 497
  • 3
  • 9
5
votes
1 answer

Can pair end reads with high heterozygosity be used to polish PacBio assembly?

I have used canu (correct) and smartdenovo to assembly PacBio reads. Next I am going to polish my assembly using illumina pair end reads by Pilon. However, I found there is high heterozygosity in my pair end reads when I used jellyfish to do k-mer…
MayWangmeiyue
  • 53
  • 3
5
votes
1 answer

Can a data file in VCF format be converted into FASTA?

I'm considering purchasing the 'MyGenome' product by Veritas Genetics to analyze my genome for a project. I'd like the data to be in FASTA format, but Veritas only provides VCF data. Is it possible to convert this VCF data into FASTA format?
WagonWheelWilly
  • 51
  • 2
5
votes
1 answer

Can I index a compressed FASTA file using STAR?

I am using STAR to align RNA-seq reads to a reference genome. Before the alignment, I need to generate an index of the reference genome. I use the following code to generate the index successfully: STAR --runThreadN 8 --runMode genomeGenerate…
Biomagician
  • 2,459
  • 16
  • 30
5
votes
2 answers

Can I use my computer while MinION is sequencing without negatively affecting the run?

I have a Mac Book Pro and I am about to start a sequencing run on the MinION. MinKNOW is going to be running for 2 days. Can I use my computer during sequencing? Can I browse the web and use Excel, etc? I am not speaking about running a…
Biomagician
  • 2,459
  • 16
  • 30
5
votes
3 answers

Is it possible to merge scRNAseq data from experiments with different design?

I have 4 different single-cell RNAseq experiments, each one representing a different sample of cell type population. I'd like to merge them to a single dataset. However, different cell types are enriched in each sample, and different samples can…
gc5
  • 1,783
  • 18
  • 32
5
votes
3 answers

Why can using more reads lead to a lower quality assembly?

I am experimenting with adding additional reads to the input files I'm giving SOAPdenovo2, and there comes a point where a good contig I've been watching actually stops showing up. Does anyone have a quick answer to why that might happen?
twmccart
  • 123
  • 1
  • 5
5
votes
1 answer

How to find which scales are available in SeqUtil of Biopython?

I am trying to analyse the hydrophobicity of a sequence using BioPython's "SeqUtil". analysed_seq = ProteinAnalysis("AKVLGSLEALEPVHYEEKNWCE") analysed_seq.protein_scale(Scale, WindowSize, Edge) Known parameters WindowSize refers to the total…
James
  • 409
  • 2
  • 13
5
votes
1 answer

What are the count units in DEseq2?

This is a pretty silly/simple question, I suppose. What units are DESeq2 counts? Or are the units arbitrary but internally consistent estimate of actual reads?
julianstanley
  • 401
  • 3
  • 9
5
votes
1 answer

What is the meaning of the Hmmer profile?

I want to understand what the hmmer Profile used in hmmer. consider the profile HMMER2.0 [converted from 3.1b2] NAME aRNH_profile LENG 121 ALPH Amino RF no CS no MAP yes NSEQ 34 DATE Tue Apr 26 21:24:57 2016 XT -8455 -4 …
A.Dumas
  • 497
  • 3
  • 9
5
votes
1 answer

Pathifier bioconductor package recommends to use technical noise for an argument. How to determine it?

I'm running the pathifier approach against C2 pathway curated database for a specific microarray dataset. As I was reading the documentation of the pathifier, in order to configure it properly for my dataset, I saw that for the min_std argument they…
J. Doe
  • 575
  • 3
  • 11
1 2 3
…
99 100