Top new questions this week:
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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 ...
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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 ...
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I have a bash script that I would like to parellelize to run on multiple nodes. My goal is to run my python sample_script.py script on pairwise comparisons of samples to see if their variants are a ...
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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 ...
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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 ...
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I am using Manta (https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md) but whenever I try to specify the --exome command using the following code ...
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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 ...
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Greatest hits from previous weeks:
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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 ...
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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 <...
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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 ...
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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 - ...
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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.
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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 ...
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I want to convert my gff3 annotation files to genbank format for use in Mauve. I found the seqret tool here https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/ which can perform this task, but my files (...
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Can you answer these questions?
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I installed the latest ucsc-bedgraphtobigwig (v377) with conda in a new enviroment enviroment inmy WSL2.
conda install -c bioconda ucsc-bedgraphtobigwig
However, ...
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I'm trying to merge two VCF files, but I'm running into an error message that says ...
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