Community Digest

Top new questions this week:

Do I have to download all nt.xx files to perform a search in blastn 2.12.0

I downloaded and extract blast nt.24 database, but when I run : blastn -task blastn-short -query consulta.fa -db nt.24 -out misalida.txt it says: mdb_env_open: No such file or directory and if a try ...

asked by Luis ALberto 1 vote
answered by Scot 0 votes

When using cutadapt, can I specify an R2 adapter as optional when I have a required R1 adapter?

I'm using cutadapt 3.5 to trim adapters and perform some filtering on paired-end data. Both R1 and R2 sequences have 3' adapters that might be found depending on the sequence length, but R1 also has ...

sequencing fastq trimming cutadapt  
asked by Jesse 1 vote
answered by Jesse 0 votes

Greatest hits from previous weeks:

R package development: How does one automatically install Bioconductor packages upon package installation?

I have an R package on github which uses multiple Bioconductor dependencies, 'myPackage' If I include CRAN packages in the DESCRIPTION via Depends:, the packages ...

r bioconductor  
asked by ShanZhengYang 13 votes
answered by Devon Ryan 9 votes

Retrieve detailed gene descriptions

Given a list of gene IDs, how do you retrieve the gene description, summary and other detailed information in R?

r gene annotation public-databases  
asked by Peter 7 votes
answered by Peter 6 votes

Converting VCF file to PLINK bed/bim/fam files

I am trying to find the best way to convert VCF files to PLINK binary bed/bim/fam files, but it seems like there are many varied ways to do this. (For example, using Plink 1.9 --vcf tag, bcftools, ...

vcf plink gatk vcftools  
asked by Sarah 10 votes
answered by gringer 6 votes

Merge hundreds of small BAM files into a single BAM file

I am working with over a million (long) reads, and aligning them to a large genome. I am considering running my alignment jobs in parallel, distributing horizontally across hundreds of nodes rather ...

alignment bam samtools  
asked by Scott Gigante 15 votes
answered by Devon Ryan 14 votes

How to subset a VCF by chromosome and keep the header?

I would like to subset a VCF which only has chromosome 2. The problem with using various grep commands, e.g. ...

vcf vcftools  
asked by EB2127 3 votes
answered by gringer 7 votes

Why do NEBNext indexing primers have sequence between the p5 oligo and index?

In a previous post I asked Why do NEB adapters have non-complementary sequence? Since then, I realized that there is some other sequence in the p5 indexing primer, as well as in the p7 indexing ...

dna illumina adapter pcr library  
asked by conchoecia 4 votes
answered by Beth Nelson 4 votes

Are variant calling files personally identifiable information?

This question is to be read in the context of data protection. It seems to be common understanding that the whole genome sequence of an individual is personally identifiable, non-anonymizable ...

vcf variant-calling  
asked by Eekhoorn 8 votes
answered by Wouter De Coster 10 votes
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