User: pbigbig

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pbigbig200
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Posts by pbigbig

<prev • 98 results • page 1 of 10 • next >
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Comment: C: miRNA quantification on custom database
... Thank you, I will check it ...
written 9 days ago by pbigbig200
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miRNA quantification on custom database
... Hi everyone, At the moment, I have some small-RNA enriched sequencing data from disease samples, read length is around 20-30 bp, tRNA largely dominated the datasets. Could you please suggest any tool(s) or tutorials for: - Extract and assemble for only miRNA or pre-miRNA - Identify and quantif ...
rna-seq mirna written 10 days ago by pbigbig200
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Comment: C: Get BUSCO gene descriptions
... Oh great! Thank you very much! Although the post was long time ago but I think it still very useful for other de novo genome project. ...
written 16 days ago by pbigbig200
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Comment: C: Calculate scaling factor for RNAseq data
... Yeah, I also thought so. However, you know that it isn't practical to write in a research proposal something for example: "we need to collect 100 brain tissues from these patients with disease and also collect dozen of fresh brain pieces from normal people just to perform RNAseq experiments at the ...
written 7 weeks ago by pbigbig200
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Comment: C: Calculate scaling factor for RNAseq data
... Yes, because I obtained them from different public databases, so 2 experiment protocols were totally different (however both data are Hiseq Illumina reads) ...
written 7 weeks ago by pbigbig200
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Calculate scaling factor for RNAseq data
... Hi everyone, I have a RNA-seq expression count matrix of 2 contrast conditions (~10 biological samples per condition), but these conditions are affected by (severe) batch effect from different sequencing experiments. I looked up for some batch-effect removal tools, but they could only fix batch-ef ...
normalization rna-seq written 7 weeks ago by pbigbig200 • updated 7 weeks ago by swbarnes26.2k
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Comment: C: Clustering differences between heatmap.2 and pheatmap
... Sorry to comment on this old post, I also just have noticed this difference when trying to create heatmaps. Do you have any suggestion on which is the better way? Clustering then scaling (like heatmap / heatmap.2) or scaling then clustering (like pheatmap), because the cluster results is quite diffe ...
written 11 weeks ago by pbigbig200
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Comment: C: which matrix should be used to draw heatmap in RNAseq?
... Thank you very much for your comprehensive answer! So as I understand, graphically in expression matrix, purpose of TPM is for same-column comparison and TMM is for same-row comparison. I think scaling by row will only benefit those who only interested in clusters of highly/lowly expressed genes in ...
written 11 weeks ago by pbigbig200
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which matrix should be used to draw heatmap in RNAseq?
... Hi everyone, I have some confusion about which type of expression matrices should I use for heatmap visualization of RNAseq data. There are 3 options listed below: (raw count matrix was obtained from featureCounts, TMM cross-sample normalization is performed by edgeR) 1. TMM-normalized raw count ...
rnaseq normalization heatmap written 12 weeks ago by pbigbig200 • updated 12 weeks ago by predeus1.2k
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Mapping both PE reads and Single-end reads into transcriptome
... Hi everybody, I built several de novo transcriptomes from non-model organism without genome reference by Trinity. Sequencing libraries were prepared with stranded method (dUTP), therefore I only used paired-end reads with RF SS_lib_type parameter in Trinity for assembling. However, earlier preproce ...
trinity strand-specific differential expression written 10 months ago by pbigbig200

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