Bioinformatics Stack Exchange
Bioinformatics Stack Exchange

Most Popular

more tags
1500 questions
3
votes
1 answer

Matlab scatter diagram

I have two columns of data, x and y, how can I make a ‘thermodynamic diagram’ with matlab? The z axis is the density value of dots, like below figure. The x-axis is angle, y-axis is distance. I want to construct a heatmap like this figure:
user239932
  • 51
  • 3
3
votes
1 answer

Highlight CpG sites with Texshade

I am using Texshade to produce figures for MSA. Upon reading the documentation I could not find anyway to highlight how conserved CpG sites within the alignment. Does anyone know if this is possible? If not is there another MSA visualizer I can use…
quantik
  • 255
  • 1
  • 9
3
votes
1 answer

What does "motif 2 bp or longer" mean?

I'm reading a preprint on a new somatic variant discovery tool, and the first sentence of the Discussion section has me confused. Across the four datasets analyzed in this study, we discovered that the major source of disagreement between callers…
Daniel Standage
  • 5,080
  • 15
  • 50
3
votes
1 answer

Interpreting large z scores from microarray data

I have microarray z scores for gene set enriched (GSE) pathways that range approximately from -3 to 14. I understand that an absolute value of 1.96 has a p-value = .05 and significant for our purposes. My question is whether I can consider extreme z…
Eddy Zavala
  • 179
  • 3
3
votes
1 answer

error in heatmap using R

I am learning about generating heatmaps using R. For this example I am using randomly generated data to test the process, but I encountered what appears to be an error or perhaps there is something am missing. Specifically, the values of Npy2r in…
Eddy Zavala
  • 179
  • 3
3
votes
3 answers

IGV jump to rsID location

Is it possible to load a list of rsID identifiers (e.g. rs66823261) to IGV to then be able to jump to the location of each of them when copy+pasting the rsID on the locus text box? For human and other genomes, there is currently the feature of…
719016
  • 2,324
  • 13
  • 19
3
votes
2 answers

How do I export my biom object to a file in biom format?

I'm using the python API for the biom-format package. I read in two files in biom format and merged them, like so: In [1]: import biom In [2]: a = biom.load_table('./table-a.biom') In [3]: b = biom.load_table('./table-b.biom') In [4]: a Out[4]:…
John
  • 147
  • 4
3
votes
3 answers

How to get UCSC Genome Browser to show the actual sequence?

Is it possible to make UCSC Genome Browser to show the sequence (nucleotide chain) of the current region? I fiddled with the various viewing options and couldn't figure it out.
Paghillect
  • 309
  • 1
  • 7
3
votes
1 answer

Why are inversions defined as the reverse complement and not just the reverse of the reference?

I can’t quite understand the way inversions are defined. In particular I expect an inversion to be only a reversed version of the reference and not its reverse complement. Most sources use diagrams such as below which totally obscure the fact that…
Paghillect
  • 309
  • 1
  • 7
3
votes
1 answer

Find Patterns in Cluster

I have a heatmap and I would like to find some rectangles. I have already used clustermap. But here, I can not calculate these rectangles. The order of the data should not be changed. This Code is not working: import pandas as pd import…
Johannes Schätzl
  • 47
  • 3
3
votes
1 answer

Dealing with indels when converting a position to chromStart and chromEnd for a bed file

Starting with a chromosome # and position, I am trying to get chromStart and chromEnd values for a .bed file, but I am not sure how to calculate chromEnd when I have a variant that is an insertion or deletion. My file is not a VCF file but it…
Sarah
  • 486
  • 1
  • 4
  • 18
3
votes
2 answers

Uniprot: Determining protein and organism given a DNA sequence

I would like to find the identity of a protein, together with the organism name and kingdom. The given DNA sequence is…
Mert Metin
  • 151
  • 3
3
votes
3 answers

Error in creating a volcano plot in MATLAB

I am a complete newbie to MATLAB and the first task I have is to create a volcano plot. I have been using this link to understand about it and get started. I tried to run it on dummy values - a=[1 2 3] b=[4.6 2.7 4.5] c=[0.05 0.33 0.45] And then…
user1995
  • 173
  • 2
  • 8
3
votes
2 answers

help with CRCmapper

I'm using CRCmapper on my data. There are several modules in the tool. I've used exactly instructed in the usage. Commands used: python CRCmapper.py -e MB12_noEncBlack_AllEnhancers.table.txt -b MB12.bam -g HG19 -f hg19-stdChr/ -s MB12_peaks.bed -n…
user1545
  • 39
  • 3
3
votes
1 answer

Installing Sibelia for Ragout on Mac OSX

I am trying to use Ragout: https://github.com/fenderglass/Ragout to fill the gaps in my de novo genome assembly. You can access the article freely here: https://www.ncbi.nlm.nih.gov/pubmed/24931998 For this, I first need to install Sibelia. I tried…
Biomagician
  • 2,459
  • 16
  • 30
1 2 3
…
99 100