User: tujuchuanli

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tujuchuanli50
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Posts by tujuchuanli

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Comment: C: can I use soft-clip RNA-seq reads to summarize gene counts?
... Thanks, michael.ante I have tried mapping with `--alignEndsType EndToEnd` and it end up dramatically decreasing the mapping percentage. ...
written 29 days ago by tujuchuanli50
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Comment: C: can I use soft-clip RNA-seq reads to summarize gene counts?
... Thanks dsull, Actually, almost of half reads are marked as soft-clip. I could lost half if I do not use these reads to summarize gene counts which I can hardly afford. The qc is somehow not very good, especially for the 3-prime end of reads. however I trim the end by qc 20 using cutadapt which didn ...
written 29 days ago by tujuchuanli50
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can I use soft-clip RNA-seq reads to summarize gene counts?
... Hi, all I have mapped RNA-seq reads using STAR (human, hg19), then I check the output bam file and find that there are many reads with cigar marked as soft-clip, such as “13S90M47S”, “88M6S” and “7S86M”. Even many of these reads also have very good flag such as “99”, “147” or “83”, “163” which indi ...
rna-seq written 29 days ago by tujuchuanli50
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Answer: A: Gene regulation network analysis mixed with other unrelated events
... Thanks a lot for your great help. ...
written 8 weeks ago by tujuchuanli50
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How to export genes with conectivity and cluster identifier in WGCNA analysis
... Hi, I used WGCNA to analyze my data and constructed network. My question is how to export genes with connectivity and cluster identifier marker. I think I may do some further detailed analysis by reading this data table. I have finished the basic WGCNA analysis including identification modules by ...
wgcna written 8 weeks ago by tujuchuanli50
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Answer: A: Gene regulation network analysis mixed with other unrelated events
... Thank you for your replying, just one further question about fold change. My original thoughts is that the effect of dysfunction of my TF are mixed with other unwanted events such as growing and tissue development along the time course. The fold change or ratio between the reads counts for one gene ...
written 8 weeks ago by tujuchuanli50
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Answer: A: selection soft Power in WGCNA
... Thank you for your wonderful discussion! ...
written 8 weeks ago by tujuchuanli50
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Gene regulation network analysis mixed with other unrelated events
... Hi, Here we investigated the regulation change of dysfunction of a TF (TF A) and try to construct the gene regulation network related to it in mouse model. Our experimental design is to take two samples (two mouse as replicates habiting the dysfunction version of TF A, case sample) every two weeks ...
network analysis written 8 weeks ago by tujuchuanli50
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Question about REDItools
... Hi, I wanted to use REDItools to identify RNA editing events in my data. I had both RNA-seq and exome-seq data derived from the same sample. I download the latest version of REDItools (REDItools-1.2.1.zip, https://sourceforge.net/projects/reditools/files/) and test data (http://srv00.recas.ba.infn ...
reditools written 10 weeks ago by tujuchuanli50
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Question about sva + edgeR to identify differentially expressed genes
... Hi, I want to identify differential genes (DEG) in TCGA dataset (cancer samples vs normal samples) by combination of `edgeR` and `sva` (get rid of batch effect by `sva`). The following is my code and I am not sure if it is ok or not. Could you please help me to check the code and give me some sugge ...
sva edger written 7 months ago by tujuchuanli50 • updated 7 months ago by ATpoint25k

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Popular Question 7 months ago, created a question with more than 1,000 views. For Correlation between gene expression and methylation

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