Bioinformatics Stack Exchange Community Digest

Top new questions this week:

Why does segmasker modify headers?

When parsing NCBI BLAST+ segmasker output, I realized the program modifies almost every header containing these strings: ( or )…

ncbi segmasker

asked by maciejwww Score of 2

Why am I not being able to detect all the bonds in a residue?

Let us consider the first seven atoms of the protein 1CRN.pdb: …

proteins protein-structure pdb 3d-structure

asked by user366312 Score of 1 answered by SuleymanSelim Score of 3

Can I perform Expression Analysis on this 10x dataset?

10x Genomics: 20k Human PBMCs is the dataset. Description of the dataset: Inputs/Libraries Human peripheral blood mononuclear cells (PBMCs) of a healthy male donor aged 30-35 were obtained by 10x …

r rna-seq python differential-expression

asked by Antonio Score of 1 answered by M__ Score of 0

Can the information regarding atomic bonds be interpreted only from atom lines in a PDB file?

The following are the first 14 atoms from the protein 1CRN: …

proteins

asked by user366312 Score of 1 answered by marcin Score of 2

file path of BiocManager:install()

I was trying to format my GWAS summary statistics with the MungeSumstats R package and would need to install …

r bioconductor reference-genome

asked by Lloyd_LiuSiyi Score of 1 answered by Maximilian Press Score of 3

Greatest hits from previous weeks:

converting mouse genes to human genes

I’m trying to convert mouse genes from PTX data to human genes in order to do a comparison with patient data to see what genes are being conserved. I’m using this file for the orthologs. www….

r seurat single-cell conversion

asked by mmpp Score of 1 answered by fra Score of 1

How to calculate p-values for fold changes?

I’m currently working with data from a Luminex multiplex assay. In this assay, the concentrations of 17 different analyte proteins were identified in 12 groups in triplicate. One of these 17 groups …

statistics

asked by J0HN_TIT0R Score of 3 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

asked by terdon Score of 12 answered by sjcockell Score of 14

How do PCR duplicates arise and why is it important to remove them for NGS analysis?

I am trying to understand PCR duplicates in NGS analyses (actually whole-genome). I searched, and the best answer I found is in this blog. However I don’t understand if I understood how PCR …

genome ngs genome-sequencing

asked by gc5 Score of 9 answered by Daniel Standage Score of 12

Why sequence the human genome at 30x coverage?

A bit of a historical question on a number, 30 times coverage, that’s become so familiar in the field: why do we sequence the human genome at 30x coverage? My question has two parts: Who came up …

genome ngs dna

asked by 719016 Score of 27 answered by chrisamiller Score of 30

How to scale the size of heat map and row names font size?

I have an expression data matrix (120X15; 15 samples and 120 genes), my heatmap looks blurred and raw names (gene names) looks very small and can not read. How can I improve my scripts? Here is the …

r rna-seq proteins clustering

asked by Kynda Score of 4 answered by sjcockell Score of 5

How can I extract normalized read count values from DESeq2 results?

The results obtained by running the results command from DESeq2 contain a “baseMean” column, which I assume is the mean across samples of the normalized counts for …

r bioconductor deseq2 normalization

asked by bli Score of 17 answered by Devon Ryan Score of 12

Can you answer this question?

segmasker doubles found intervals

During NCBI BLAST+ segmasker output exploration, I found out that for some sequences, the program returns the same interval twice: …

ncbi segmasker bugs

asked by maciejwww Score of 1