User: bioinfo_wen

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Posts by bioinfo_wen

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Should I remove zero-value from my single cell expression matrix before doing differential test?
... If I have an expression matrix with 2 conditions, A and B, and 30 cells in A condition, 40 cells in B condition. And I want to perform wilcoxon rank sum test for each gene in this matrix, Is it ok to perfor following pre-processing steps? 1. Cutoff setting: Only a gene expressed in at least 5 cells ...
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how to distinguish pre-mRNA and mature mRNA from my nuclear RNA-seq data?
... AS we know, most pre-mRNAs were retained in nucleus and after processing such as alternative splicing, it was transported into cytoplasm. However, there are also some mature mRNA/lncRNA exists in nucleus. If I have my nuclear samples sequenced, how could I seperate mature mRNA and pre-mRNAs from my ...
rna-seq nucleus pre-mrna mature mrna written 10 weeks ago by bioinfo_wen0
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Is it OK doing Principal component analysis (PCA) analysis just with high variance genes?
... There are so many papers performing PCA analysis with only top high variance genes(top 500 for example), and the plot seems good. Cells in different conditions separated from each other, but I am wondering is that reasonable? Since all the genes in my expression data can represent all the characteri ...
pca written 11 weeks ago by bioinfo_wen0 • updated 11 weeks ago by Hussain Ather860
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Comment: A: FastQC results with abnormal GC content and Overrepresented sequences in RIP-seq
... There are 2 replicates sample in my RIP-seq for each condition, but another sample performed better than this. I maped my reads to mm10 with hisat2, the overall mapping rate about 69%,and nearly 50% of total reads aligned concordantly exactly 1 time. sequencer was illumina Hiseq 3000, And I am wonde ...
written 3 months ago by bioinfo_wen0
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FastQC results with abnormal GC content and Overrepresented sequences in RIP-seq datasets
... my mouse RIP-seq data have abnormal GC content and the fastqc result in 'GC content' have 2 peaks, first one is about 55% in x axis, y axis is about 500000. the second one as about 85% in axis,y axis is about 1600000, very sharp peak.besides, the GC content each base is not about 25% for A,T,G,C. th ...
fastqc gc-content rip-seq written 3 months ago by bioinfo_wen0

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