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Is it possible to check if a patient has the HLA-B27 antigen from his exome stored in a VCF file

Is it possible to check if patient has the HLAB27 antigen by comparing his exome stored in VCF with all known HLAB27 variants? For instance, rs4349859 is a known HLAB27 SNP. If I can find rs4349859 in the patient's VCF file, could I say he is…
marcos
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CRISPR Sequence Finder and Database Download

I am searching for tools to pull CRISPR Spacers from Bacterial Genomes. I am aware of the CRISPRDB and the corresponding identification tool on the web server. Are there other tools for finding CRISPR Spacers? Is there a way to download the spacer…
Cody Glickman
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LD analysis in PLINK based on reference and a SNP list

I'm new to PLINK and genetics, and getting confused with two PLINK commands for LD analysis: plink --bfile hapmap --r2 --ld-window-r2 --ld-snp-list --ld-window plink --noweb --bfile --clump hapmap --clump inputfile --clump-field P --clump-p1…
Rob John
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About CAFA experiment

I have a question about CAFA1 and CAFA2 experiment. CAFA is an experiment that compare computational methods predicting protein functions. In the paper discussing CAFA2, there is an image comparing 2 methods (CAFA1 versus CAFA2): How do I…
Amine
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2 answers

Interpreting 0x200 flag in bwa-mem alignments

I am looking at the bwamem.h code in http://github.com/lh3/bwa and found that BWA-MEM will give flag 0x200 to what it calls MEM_F_SOFTCLIP: #define MEM_F_PE 0x2 #define MEM_F_NOPAIRING 0x4 #define MEM_F_ALL 0x8 #define MEM_F_NO_MULTI …
719016
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How to get Nanopore MinION fast5 from SRA

I found some Nanopore MinION data on SRA, which I would like to investigate. I use sratoolkit for Illumina data all the time, but I am not sure how to get the fast5 file from the sra file. What I have tried is to prefecth it, but then I don't know…
benn
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Estimating BAM file from compressed fastq file size

Is there a way to estimate the size of a BAM file will have after mapping with BWA? The input file are two mates fastq files, compressed with gzip, each one about 70G.
gc5
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bcftools output vs. bgzip

I've got what seems like it should be a simple question, but I can't seem to figure it out from google. bcftools has 4 output options: Output compressed BCF (b), uncompressed BCF (u), compressed VCF (z), uncompressed VCF (v). Are any of these the…
heathobrien
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Is there any publicly available multi-omics dataset?

I am searching for a multi-omics dataset which may include genomics, transcriptomics and proteomics (eg. snyderome). I need such a dataset for an introductory data-exploration purpose. So it can be from any host organism and any experimental…
user345394
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How to query a network for a bacterium, specifically Streptomyces caatingaensis or Streptomyces thioluteus?

I have a list of gene/protein IDs and I could not query a network using String, BioGrid, Intact and IIS, for Streptomyces thioluteus. The bacteria I am working with is the Streptomyces caatingaensis. Since it is newer than others, I thought I would…
Henry
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What is local realignment and what is the problem it solves?

I am trying to understand local realignment but I could not get a clear idea of what is the problem solved by it. For example, reading Homer and Nelson (2010): Because alignment algorithms map each read independently to the reference genome,…
gc5
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RapMap: reference transcriptome for simulated reads

I am very new to bioinformatics and trying to repeat the benchmark in the RapMap paper with an experimental tool working in a similar but different fashion. In the paper (taken from their github) about RapMap, an alignment/mapping tool for rna-seq…
JMC
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2 answers

BiomaRt error: Error in martCheck

I am experiencing an error while using getSequence() in biomaRt. The code is given below: library("biomaRt") ensemblp <- useMart(biomart="plants_mart",host="plants.ensembl.org") osj = useDataset("osativa_eg_gene", mart = ensemblp) genes <-…
Learner
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How can I specify to DEseq2 to only perform comparisons on which I am interested with?

I am currently performing a large RNA-seq analysis from mice PBMCs. The dataset contains around 6,000 transcriptomic profiles and I would like to use DESeq2 to identify the sets of differentially expressed genes in the different conditions. In…
Bob
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Differential Expression With 2 Treatments

I have a expression data from a small cohort of samples taken at baseline and after 2 independent treatments. I can do differential expression contrasting T1 and T2 or I can contrast T1 vs baseline and T2 vs baseline and look at the differences.…
Nitro
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