Community Digest

Top new questions this week:

WGBS vs ONT, which one should I trust?

First of all let me apologize if this is not the place for this question. While it can be quite broad, I will try to make it as specific as I can. Context I am testing the correlation between Whole ...

methylation epigenetics  
asked by Paul Endymion 2 votes
answered by gringer 2 votes

PacBio long-reads impact in transcriptome de novo assembly?

We are strongly interested in assembly a good transcriptome of reference for a non-model organism and build a local database. We have sequenced the same individual with Illumina (150 millions of pair-...

rna-seq assembly transcriptome long-reads  
asked by Manuel Sánchez Mendoza 1 vote
answered by Bastian Schiffthaler 2 votes

Performing PCA for the samples and for the genes

I have 10 samples from a RNAseq experiment (5 control, 5 disease), I have performed a cluster analysis for the samples and for the genes (4000 genes aprox) to see how they cluster (to see which ...

pca  
asked by Mee 1 vote
answered by haci 2 votes

dbnSNP frequency anomalies

Sometimes dbSNP reports very different allele frequencies for different large-scale genome projects e.g. between 1000 Genomes and GnomAD rs11822440 1000Genomes A=0.4629 C=0.5371 GnomAD A=0.99997 ...

snp 1000genomes  
asked by afaulconbridge 1 vote
answered by Michael 0 votes

Greatest hits from previous weeks:

SNP vs Point Mutation

What is the difference between a Single Nucleotide Polymorphism (SNP) and a point mutation? I am quite confused in understanding these term as both of them refer to one base difference from the ...

snp terminology variation  
asked by Zheng Keong Ng 5 votes
answered by finswimmer 4 votes

What's a template switching site?

Reading Islam et al. (2011): From each transcript, a single read is obtained, corresponding to a template-switching site located preferentially at the 59 end of the mRNA. By reading this page I ...

scrnaseq  
asked by gc5 6 votes
answered by plat 5 votes

How can I downsample a BAM file while keeping both reads in pairs?

I know how to downsample a BAM file to lower coverage. I know I can randomly select lines in SAM, but this procedure can't guarantee two reads in a pair are always sampled the same time. Is there a ...

bam  
asked by medbe 16 votes
answered by rightskewed 14 votes

Difference between samtools mark duplicates and samtools remove duplicates?

What is difference between samtools mark duplicates and remove duplicates ? Is it necessary to mark duplicates before removing duplicates with samtools?

alignment ngs samtools  
asked by Ammar Sabir Cheema 5 votes
answered by Kohl Kinning 3 votes

What is a quick way to find the reverse complement in bash

I have a DNA sequence of which I would like to quickly find the reverse complement. Is there a quick way of doing this on the bash command line using only GNU tools?

sequence-analysis dna bash  
asked by winni2k 6 votes
answered by winni2k 14 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

What are doublets in single cell RNA-seq data?

I am reading The Tabula Muris Consortium et al. (pp). In some organs, cells with more than 2 million reads were also excluded as a conservative measure to avoid doublets. How exactly is a “doublet”...

scrnaseq single-cell quality-control  
asked by gc5 6 votes
answered by gringer 7 votes
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