Bioinformatics Stack Exchange
Bioinformatics Stack Exchange

Most Popular

more tags
1500 questions
5
votes
1 answer

Ancestry of the coronavirus 2019-nCov, WuHan city, China

In one of the answers to another question about the corona virus a link was given to this phylogenetic analysis of the virus. Can somebody assist a non-bio type here? It seems to show that the current corona virus split from a virus in bats. And…
puppetsock
  • 153
  • 3
5
votes
1 answer

Are there any "canonical" sources of C. elegans connectome?

I found that there are a couple of projects that allow the user to simulate the neural system of C elegans, for example OpenWorm one update being here. I don't know how to navigate sources in bioinformatics and thus struggle to evaluate their…
d33tah
  • 151
  • 3
5
votes
1 answer

which NCBI tool is optimized to identify a species from a DNA fragment?

“The Iceman” was a man who lived 5300 years ago and whose body was recovered from an Alpine glacier in 1991. Some fungal material was recovered from his clothing and sequenced. Ice man : found as a frozen corpse in the Val Senales Glacier in Italy.…
CodeDependency
  • 51
  • 2
5
votes
1 answer

Find covariation of different DNA-binding protein binding between two conditions

I have ChIP-seq data of RNAPII and two other factors which we think follow RNAPII during transcription in two different conditions, and I'd like to show that the genes that lose RNAPII also lose the other two factors, and same for gains. Do you know…
Whitehot
  • 300
  • 1
  • 9
5
votes
4 answers

tool to visualize a collection of phylogenetic trees

I have a collection of phylogenetic trees produced from clustering DNA sequences, mostly a few nodes in each cluster/tree, with several clusters of size 1. And I would like to visualize them all together to get an idea of the relative sizes of the…
719016
  • 2,324
  • 13
  • 19
4
votes
1 answer

snakemake with --conda-prefix, can I use a pre-built conda environment?

I have read this question (Running Snakemake in one single conda env) but still have some doubt. I am using the '--conda-prefix /some/dir' option and I have a rule in my snakemake file with the directive: rule xxx: ... conda: …
guibar
  • 143
  • 3
4
votes
2 answers

How to convert a phylogeny to a dendrogram in R

I want to convert my phylogeny into a dendrogram so I can use it with dendextend in R to produce a tanglegram. I have made some progress but I keep encountering errors, see below: library(ape) library(dendextend) Tree <- rtree(10, rooted=F) Tree…
AudileF
  • 955
  • 8
  • 25
4
votes
5 answers

Fix dash/empty ALT alleles for deletions in VCF

I have a VCF file that has deletions specified like this, with the REF allele containing only the deleted portion and the ALT allele just saying -: chr1 101 . AAA - I would like to combine this with another VCF in which deletions are specified like…
Nils
  • 315
  • 1
  • 7
4
votes
3 answers

PDB codes for misfolded proteins?

I'm searching for PDB code examples for "healthy proteins" and misfolded ones, so I can compare the 3D structure. I'd prefer pairs of a "protein misfolding disease", but could be any. Can I find such a list or how should I search for the particular…
Jake B.
  • 205
  • 1
  • 4
4
votes
1 answer

In SBOL, when should I annotate a DNA sequence vs. making sub-components?

When representing a DNA sequence in SBOL as a ComponentDefinition, you can mark things like promoters and coding sequences in two different ways: either as a SequenceAnnotation in the ComponentDefinition, or as a Component linking to a…
jakebeal
  • 653
  • 4
  • 16
4
votes
1 answer

How to get a MSA fasta from BAM/SAM?

I am working with paired end NGS miseq data from a viral genome with multiple timepoints. I have filtered and trimmed this data for quality and adapter sequences. I have then merged the filtered paired end reads and mapped them to a reference…
Lvl1
  • 41
  • 1
4
votes
1 answer

Using `install.packages` with conda-managed R

I have R installed and managed by conda (miniconda) on my MacBook Pro. The version of R I use most frequently (3.5.1) is installed on the base environment and I have other version-specific environments as well. I did this as it was easier than…
Ram RS
  • 2,297
  • 10
  • 29
4
votes
1 answer

What do the read colors in IGV mean?

I was looking at a bam file in the IGV viewer and saw: What do the different read colors mean? Why is one read a light blue color, another green, another aquamarine (?), another purple and another two orange? What do these different read colors…
terdon
  • 10,071
  • 5
  • 22
  • 48
4
votes
3 answers

What do the FASTQ file names mean here?

I would like to run an analysis on Nanopore data. I'm trying to download sample data from https://github.com/nanopore-wgs-consortium/chm13. I would like to run minimap2 on the FASTQ files, resulting in a single BAM file. Q: What do the file names…
SmallChess
  • 2,699
  • 3
  • 19
  • 35
4
votes
2 answers

Mixcr batch processing

I have a folder with 150 pairs of fastq files from an illumina sequence run. I need to precess them with mixcr, how can I do this in Bash with a single command?
Lou_A
  • 361
  • 1
  • 4
  • 11
1 2 3
…
99 100