User: weiyanjia2008

gravatar for weiyanjia2008
Reputation:
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New User
Location:
USA/Madison/UW-Madison
Last seen:
5 days, 9 hours ago
Joined:
3 years ago
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w************@gmail.com

Posts by weiyanjia2008

<prev • 14 results • page 1 of 2 • next >
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How to speed up computeMatrix of deeptools?
... When I do`computeMatrix` using all gene regions and extent to 0.5Mb of TSS for Replication timing signal analysis, it has been running for two days. Is there any setting that can speed up the running or other alternative tools to do this? The code is as follow: BIN=20000 WIN=500000 RBL ...
software error written 3 months ago by weiyanjia200830
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Comment: C: IGV error: Error reading BBFile header for bw files
... Thanks! I checked my JAVA version: > java -version java version "13.0.1" 2019-10-15 Java(TM) SE Runtime > Environment (build 13.0.1+9) Java HotSpot(TM) 64-Bit Server VM (build > 13.0.1+9, mixed mode, sharing) Still not working and not sure what's the problem. IGV on Mac still can open b ...
written 9 months ago by weiyanjia200830
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IGV error: Error reading BBFile header for bw files
... I met this error when I try to visualize bw files created by tool bedGraphToBigWig after sorting.The bedgraph files were generated by STAR. The error: "Error loading /Users/weiyanjia/W_T_1.bw: Error reading BBFile header for: /Users/weiyanjia/W_T_1.bw" I am using the lasted version of IGV(2.7.2) and ...
bw igv written 9 months ago by weiyanjia200830 • updated 6 months ago by bhanratt40
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Comment: C: nperm value in GSEA setting
... Thank you very much for your reply. That's the answer what I need "Increasing the permutations shouldn't take a non-significant gene set and make it significant" Best ...
written 15 months ago by weiyanjia200830
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nperm value in GSEA setting
... I am wondering does it matter to set the nperm value from 1000 to 100000 or even higher? I do see higher value of nperm will give a lower q value. I saw most of the papers or tutorials will use 1000. The nature Protocols paper(Reimand, J et al. (2019). Pathway enrichment analysis and visualization ...
gene rna-seq written 15 months ago by weiyanjia200830 • updated 15 months ago by shawn.w.foley1.2k
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Comment: C: problem with create design in edgR
... Hi Friederike, Thank you very much. As you suggested, there is something wrong with my group setting. Best, Weiyan ...
written 19 months ago by weiyanjia200830
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problem with create design in edgR
... Hello, I have two groups WT and KO, each has 3 replicates. I followed this paper: http://master.bioconductor.org/packages/release/workflows/vignettes/RNAseq123/inst/doc/limmaWorkflow.html everything is going well until I did the design step: The code is design <- model.matrix(~0+group) ...
rna-seq written 19 months ago by weiyanjia200830 • updated 19 months ago by Friederike6.3k
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Comment: C: Rsubread: Aligning multiple paired-end files
... Hello, when I run this script I get the ERROR: unable to open file 'NA'. File name might be incorrect, or you do not have the permission to read the file. ibrary(Rsubread) reads1 <- list.files( path="/home/weiyan/Desktop/RNA_SEQ/files/fastq/trimmed/rif1", pattern = "*_1.fq.gz$" ) rea ...
written 20 months ago by weiyanjia200830
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Comment: C: Where to download blacklisted regions?
... Thank you very much! It works right now. ...
written 2.1 years ago by weiyanjia200830
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Comment: C: Where to download blacklisted regions?
... When I use this file as a blacklist to run deeptools-bamcompare, it was reported this list has overlaps. chr16 34586660 34587100 chr16 34587060 34587660 My understand is the bottom range overlaps with the top one. 34587060 < 34587100 ...
written 2.5 years ago by weiyanjia200830

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