Top new questions this week:
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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 ...
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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-...
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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 ...
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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 ...
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Greatest hits from previous weeks:
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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 ...
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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 ...
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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 ...
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What is difference between samtools mark duplicates and remove duplicates ? Is it necessary to mark duplicates before removing duplicates with samtools?
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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?
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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 ...
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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”...
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