Community Digest

Top new questions this week:

What is the NCBI's definition of an "atypical genome"?

Using the new NCBI Datasets platform, you can browse the collection of genomes associated with one or more taxa. For example, searching Pseudomonas aeruginosa returns 19,878 genomes as of 29 March ...

genome data-download ncbi  
user avatar asked by acvill Score of 4
user avatar answered by acvill Score of 2

Passing strings for password, email authentication and download link

Hi I am downloading the data from a website which requires authentication of email_id and password before the download. They then provide the download link which is used to download dataset. This ...

database bash curl  
user avatar asked by Priya Score of 3
user avatar answered by Steve Score of 3

Parallelize or qsub a bash script

I have a bash script that I would like to parellelize to run on multiple nodes. My goal is to run my python script on pairwise comparisons of samples to see if their variants are a ...

python bash parallel  
user avatar asked by che625 Score of 2
user avatar answered by Pallie Score of 4

RNAseq alignment: best practices for aligning to multiple isoforms?

I have Illumina RNAseq data and would like to maximize my power to find candidate genes that are differentially expressed genes between experimental conditions. Many of my (de novo assembled and ...

rna-seq sequence-alignment deseq2 differential-expression isoform  
user avatar asked by DavidR Score of 2
user avatar answered by Alexlok Score of 0

Dealing With Manta Limitations

I am trying to figure out a way to remove the limiting factors that Manta says it cannot handle. To quote from the Manta page: The following limitations exist on the input BAM or CRAM files provided ...

sam bash  
user avatar asked by Indira Score of 2
user avatar answered by Steve Score of 1

Manta "--exome: command not found"

I am using Manta ( but whenever I try to specify the --exome command using the following code ...

bash exome  
user avatar asked by Indira Score of 2
user avatar answered by Ram RS Score of 4

Using ticks on the x axis or a scale bar when visualisizing a phylogram?

When visuliazing a phylogram is it preferable to show ticks on the x axis or a scale bar? Given an example tree with branch lengths in newick format ...

phylogenetics phylogeny visualization  
user avatar asked by Tony Score of 2
user avatar answered by M__ Score of 1

Greatest hits from previous weeks:

Formula for k-mer coverage

Let $C$ be base coverage, $R$ is the length of reads and $K$ is the length of $k$-mer. Then $k$-mer coverage $C_k$ can be computed as $C_k = C\cdot(R - K + 1)/R$. Could someone please explain why is ...

user avatar asked by user44697 Score of 8
user avatar answered by Devon Ryan Score of 3

Fast way to count number of reads and number of bases in a fastq file?

I am looking for a tool, preferably written in C or C++, that can quickly and efficiently count the number of reads and the number of bases in a compressed fastq file. I am currently doing this using <...

ngs fastq software-recommendation benchmarking  
user avatar asked by terdon Score of 12
user avatar answered by sjcockell Score of 14

How to subset a BAM by a list of QNAMEs?

I have a text file 'qnames.txt' with QNAMEs in the following format: EXAMPLE:QNAME1 EXAMPLE:QNAME2 EXAMPLE:QNAME3 EXAMPLE:QNAME4 EXAMPLE:QNAME5 I would like to ...

sam samtools  
user avatar asked by EB2127 Score of 8
user avatar answered by Bioathlete Score of 4

How to obtain .bed file with coordinates of all genes

I want to get a .bed file with the genes' names and canonical coordinates, also I would like to have coordinates of exons, too. I can get the list from UCSC, however, if I choose UCSC Genes - ...

bed public-databases  
user avatar asked by German Demidov Score of 14
user avatar answered by Alex Reynolds Score of 15

Variant vs Allele vs SNP

Coming from a CS background. Reading through the wikipedia page, these all sounds like the same thing: Variant, Allele, and SNP. Variant/Allele/SNP: Some gene locus that differs from the idea human. ...

user avatar asked by Matthaeus Gaius Caesar Score of 4
user avatar answered by Emily_Ensembl Score of 4

Why Ti/Tv ratio?

I'm interested in the transition/transversion (Ti/Tv) ratio: In substitution mutations, transitions are defined as the interchange of the purine-based A↔G or pryimidine-based C↔T. Transversions are ...

user avatar asked by SmallChess Score of 9
user avatar answered by user172818 Score of 8

Existing tool for converting gff3 to genbank (gbk)

I want to convert my gff3 annotation files to genbank format for use in Mauve. I found the seqret tool here which can perform this task, but my files (...

format-conversion gff3 genbank  
user avatar asked by Mark Score of 4
user avatar answered by Felipe Almeida Score of 3

Can you answer these questions?

ucsc-bedgraphtobigwig throwing memory allocation error

I installed the latest ucsc-bedgraphtobigwig (v377) with conda in a new enviroment enviroment inmy WSL2. conda install -c bioconda ucsc-bedgraphtobigwig However, ...

user avatar asked by ricardo3889 Score of 1

Title: Error merging VCF files: "The REF prefixes differ: G vs A"

I'm trying to merge two VCF files, but I'm running into an error message that says ...

vcf merge  
user avatar asked by El K Score of 1
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