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1500 questions
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2 answers

Sort vcf by contig and position within contig

Due to tabix constraints, I need to sort a vcf so that contigs and then positions within contigs occur in numerical order in the vcf. I don't know if the following will sort positions within contigs, but I tried this: cat in.vcf | vcf-sort -c >…
Peter Pearman
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SNP vs Point Mutation

What is the difference between a Single Nucleotide Polymorphism (SNP) and a point mutation? I am quite confused in understanding these term as both of them refer to one base difference from the reference sequence?
Zheng Keong Ng
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making my own population allele frequency table for input to IADMIX from Gnomad data (population admixture)?

Hi I'm a first time user of IADMIX. I tested on one known Finnish sample from the 1000Genome project using the softwares provided frequency table hapmap3.8populations.hg19.freqs and the prediction is correct. I'm also want to do the same using…
Sam
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1 answer

Proof of Breakpoint Reversal Sorting Approximation Algorithm

I'm kind of new to bioinformatics and trying to self-study. I'm reading a bioinformatics book: An Introduction to Bioinformatics Algorithms and ran into some problems about understanding the proof of the Breakpoint Reversal Sort algorithm in chapter…
Hang Le
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6
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1 answer

How to run HYPHY on multiple files non-interactively?

I would like to test for positive selection in a large set of genes. I want to have a yes/no answer to the question if gene was evolving under positive selection. Therefore I chose model BUSTED for my analysis, which is implemented in HYPHY. When I…
Iakov Davydov
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6
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Is it possible to calculate p-values for fold changes of single replicate RNA-seq samples?

I'm thinking that this isn't actually possible, but I'd like to check before I write it off. I have RNA-seq data from cells under three different conditions, there are no replicates for any of the conditions. The data has been processed with RSEM,…
J0HN_TIT0R
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6
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1 answer

How do I compare measured ratios to calculated ratios in peptide mass spectrometry?

I have two different sets of internal standards in a sample (1), and a sample (2) with these internal standards as well as about 30 peptides. Each peptide has one of each of these kind of standards. From sample 1, I can get the true ratio between…
Max Jonatan Karlsson
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6
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1 answer

Can a customized GRCh38 .gtf file be used with any of the GRCh38 released patches?

I got a customized GRCh38.79 .gtf file (modified to have no MT genes) and I need to create a reference genome out of it (for 10xGenomics CellRanger pipeline). I suspect that the .79 part is the Ensembl number, which according this ensembl archive…
Glrs
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Can't install newest Blast from Conda

I have run into an odd situation, where Anaconda repo page clearly states that the newest version of Blast in Bioconda channel is 2.7.1, however the version Conda wants to install (command conda install -c bioconda blast) is 2.6.0. Even specifying…
user44697
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1 answer

What is Allelic Imbalance

Can anyone help me explain what allelic imbalance is, hopefully shortly? Surprisingly, we cannot find any introduction online.
Haohan Wang
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6
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1 answer

Detecting portions of human proteins with high degree of microbial similarity

I'm a newcomer to the world of bioinformatics, and in need of help solving a problem. My goal is to take a list of human proteins, and identify segments (13-17aa in length) with a high degree of similarity to microbial sequences. Ideally, I would…
bluescholar1212
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0 answers

Why does repeatmasker annotate transposons of length 1?

I am working on Mac OSX. I have downloaded RepeatMasker from www.repeatmasker.org. I have downloaded RepBase from www.girinst.org. I have download the WS266 version of the C. elegans genome from WormBase. I have installed nhmmer using conda. I have…
Biomagician
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1 answer

What is the minimum number of individuals per group required for ADMIXTURE analysis?

What is the minimum number of individuals required per group (population/species) for an ADMIXTURE analysis to be appropriate? Is there a way to determine this number mathematically based on the amount of genetic data I have or other criteria? Are…
Erin Thompson
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6
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3 answers

Total reads aligning to each reference within a bam file

I have two PCR amplicons that have been multiplexed and sequenced using the nanopore minion. I have aligned the fastq reads using minimap2 with a reference file containing both amplicon sequences and generated a bam file that I have viewed using…
CM3
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5 answers

Delete all 4 lines of a fastq read from a fastq file using read ID

I have the following error when running bowtie2: Error: Read HWI-D00466:116:CC62WANXX:3:1102:7363:63646 1:N:0:GCACACG has more read characters than quality values. I now want to remove all 4 lines of this specific read from the fastq file. How…
T. Ntsowe
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