Community Digest

Top new questions this week:

installing multiple bioconductor packages at once

I was wondering if there is more elegant way of installing and loading multiple packages in Bioconductor similar to pacman with CRAN packages. I tried: ...

bioconductor  
asked by Sam 4 votes
answered by ATpoint 3 votes

How to import large bed, gff, vcf files into SQL databases?

Are there best practices of loading different bioinformatics file formats such as VCF, BED, and GFF to an SQL database? I am wondering how people out there do that efficiently. All of these three ...

database bed data-management gff tabix  
asked by 0x90 2 votes

Why is the UniProt REST API returning multiple results, when I am only providing one ID to be checked?

Can some explain why when I run a REST API query on UniProt for one ID ('Q9UJL9'), the results for three IDs are returned? The query I'm using is: https://www.uniprot.org/uniprot/?query=Q9UJL9&...

uniprot api  
asked by Slowat_Kela 2 votes
answered by Jerven 2 votes

How to programmatically classify a protein according to its genbank feature

Say I found an interesting protein in a genbank file, e.g.: ...

annotation uniprot genbank gene-ontology  
asked by Oren Milman 2 votes

Find pattern that is present twice and allow <=2 mismatches on each

I have a fastq file of 400,000 reads (so speed is important). In the sequences there are barcodes integrated that should be present twice. Given a barcode, I want to find the sequences that have the ...

sequence-alignment fastq long-reads bioawk barcode  
asked by nafizh 1 vote

Retrieve overlap widths with Bioconductor

I want to retrieve all overlaps between two sets of genomic intervals (GRanges) using Bioconductor. I am interested in the widths of the resulting overlapping ranges. In cases with discontinuous ...

r bioconductor genomicranges  
asked by cmdoret 1 vote
answered by Sebastian Müller 1 vote

Greatest hits from previous weeks:

FeaturePlot from Seurat: change its title

FeaturePlot is a function in Seurat package. And in the vignette it is written that if we specify parameter do.return = TRUE it ...

r ggplot2 seurat  
asked by Nikita Vlasenko 7 votes
answered by plat 3 votes

Can open-source software be peer-reviewed and published?

My colleague and I have developed a software tool intend to release it open-source. This tool is specifically for tasks in bioinformatics but we think it would be helpful for the wider community. Our ...

publishing  
asked by Tom Kelly 12 votes
answered by Devon Ryan 12 votes

Are mitochondrial genes to exclude in scRNA-seq such as ribosomal genes?

In this answer, it is stated that ribosomal genes should be excluded prior to normalization in scRNA-seq as contaminants. Do mitochondrial genes have to be excluded as well? I plotted the top 50 ...

rna-seq scrnaseq quality-control  
asked by gc5 7 votes
answered by gc5 5 votes

RNAseq: Z score, Intensity, and Resources

I'm very new to bioinformatics in general, and I'm trying to understand some basic concepts. I have RNAseq data, and bioinformatics people tell me that intensities cannot be compared across patients. ...

rna-seq bioconductor python normalization  
asked by julianstanley 4 votes
answered by benn 3 votes

What is the index fastq file (sample_I*.fastq.gz) generated when demultiplexing Illumina paired-end runs?

What is the index fastq file that comes with some Illumina sequencing datasets? (The samplename_I*.fastq.gz file.) For example, I recently received some 10X ...

sequencing illumina 10x-genomics demultiplexing  
asked by conchoecia 8 votes
answered by conchoecia 7 votes

Remove/delete sequences by ID from multifasta

I have a fasta file like this: >Id1 ATCCTT >Id2 ATTTTCCC >Id3 TTTCCCCAAAA >Id4 CCCTTTAAA I want to delete sequences that have the following IDs. <...

fasta shell  
asked by andresito 6 votes
answered by Alex Reynolds 6 votes

How to convert BED to GFF3

I would like to convert a BED format to GFF3. The only useful tool that I could find via a google search seems to be Galaxy, ...

software-recommendation bed format-conversion gff3  
asked by aechchiki 12 votes
answered by Severian 6 votes
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