Bioinformatics Stack Exchange
Bioinformatics Stack Exchange

Most Popular

more tags
1500 questions
3
votes
2 answers

Minion channel ID's from Albacore

The latest version of Albacore from Oxford Nanopore Technologies calls bases from raw fast5 files. A useful piece of output is the sequence_summary.txt, which is a big tab-delimited file with information on each read. One of the columns in there is…
roblanf
  • 962
  • 7
  • 15
3
votes
1 answer

Viral genome finishing

I have assembled poxvirus genome using Ray. The assembly is good. Out of several thousand contigs I got, I was able to get one scaffold using Contiguator tool, which is about 90% of my genome. I have well annotated reference sequence. If there any…
L R Joshi
  • 719
  • 3
  • 11
3
votes
1 answer

How to filter blast results from blast run against virulence factor database

I downloaded virulence factor database from here , to predict virulence genes from few genomes that my lab sequenced. I performed local blast on the database with default setting and found around 4000 genes. I want to filter this result. I am not…
Ahmed Abdullah
  • 367
  • 2
  • 8
3
votes
2 answers

How to use busco installed through conda?

I have installed busco on my Mac computer using conda install --channel bioconda busco=3.0.2 into an environment called busco3_0_2. However, when I type busco, the command is not found. Anyone knows what the name of the binary is? Usually when I…
Biomagician
  • 2,459
  • 16
  • 30
3
votes
1 answer

Why doesn't the mouse GRCm38/mm10 refGene genome annotation file contain non-coding transcripts?

I am new to Bioinformatics and I am exploring the refGene.txt files from the UCSC genome annotation database for several species. My question concerns the Dec. 2011 (GRCm38/mm10) assembly of the mouse genome. I have seen that the Human one (hg39)…
jorvaor
  • 49
  • 4
3
votes
1 answer

load the phenotype data for ballgown

I am trying to reproduce the work of this paper [1], and I have run StringTie successfully, but after that I have to run Ballgown but could not understand this command: >pheno_data = read.csv("geuvadis_phenodata.csv") Actually, I dont know how to…
fatima
  • 31
  • 2
3
votes
1 answer

Storing FindAllMarkers results in Seurat object

I am currently working on multiple datasets where each is managed by a separate Seurat object. For each I'd like to also compute the marker genes using the FindAllMarkers function. Where would it be a good practice to save the markers returned from…
Gilad Green
  • 135
  • 7
3
votes
1 answer

What is the difference between a MeSH concept and a MeSH descriptor

Medical Subject Headings (MeSH) is a very comprehensive vocabulary to index the biomedical literature on Medline or PubMed (which is the major Biomedical literature database). MeSH is arranged into Descriptor > Concept > term hierarchy, but I still…
PinkBanter
  • 201
  • 1
  • 5
3
votes
1 answer

RNA-seq analysis of mixed viral/host reads with salmon

I did RNA-seq of mammalian cells infected with pox virus. Now, I have read files which contain both host and virus reads. I want to align the reads both to host and viral genome. I was thinking I could concatenate the host and virus genome into one…
L R Joshi
  • 719
  • 3
  • 11
3
votes
2 answers

mapping heteryzygous kmers on a genome

I have a set (a couple of millions) of kmer pairs of known length (usually 21) that I know that are heterozygous in the middle nucleotide. For instance: AAAAAAAAAANAAAAAAAAAA Where N has always two states. I would like to map these nucleotides on a…
Kamil S Jaron
  • 5,542
  • 2
  • 25
  • 59
3
votes
1 answer

Pipeline for extracting gene from multiple genomes for use in HyPhy selection analyses?

I have been trying to obtain some preliminary data from HyPhy selection analyses to inform a larger project. I have obtained a number of assembled mammalian genomes from NCBI with the initial goal of extracting from each of them their corresponding…
PollardMD
  • 79
  • 3
3
votes
1 answer

How to interpret UniProt allele patterns?

In creating a parser for the UniProt flat file uniprot_sprot.dat (directory) in the manual for the comments POLYMORPHISM there are listed patterns for alleles, e.g. for 1A11_HUMAN is The following alleles of A-11 are known: A*11:01 (A-11E),…
Guy Coder
  • 315
  • 1
  • 9
3
votes
2 answers

Is there a safe catch-all adapter sequence for trimming?

I would like to trim/mark adapters using trimmomatic or picard MarkIlluminaAdapters from a series of Illumina Paired-End read fastqs. The fastq files may have been done using different kits or different generations/versions of illumina…
init_js
  • 319
  • 2
  • 9
3
votes
0 answers

I am getting a parsing error when uploading .chip file to GSEA software

I get the following error when I try to load a .chip file to GSEA software. What is the problem? ---- Full Error Message ---- There were errors: ERROR(S) #:1 Parsing trouble java.lang.NumberFormatException: ... ---- Stack Trace ---- # of…
ham123
  • 51
  • 2
3
votes
0 answers

Differentially methylated position analysis in a related sample?

I'm trying to figure out how to do a DMP analysis (using minfi dmpFinder) on a related sample (if it's even possible). Right now the code (not written by me) is: dmps = dmpFinder(mVals, pheno = targets1$X8yrfactor, …
Hayley Sowards
  • 31
  • 2
1 2 3
…
99 100