User: bioinfool

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bioinfool20
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Posts by bioinfool

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Comment: C: Easy way to run easily orthoMCL (Copy & paste)
... That's the resulting output of blastdb. It just make the database for you. After that, you need to run it in blastp. The blastall is included in the old blast version. The new one do not really have the blastall command. I think it's okay to just run blastp. Well, yeah. ...
written 28 days ago by bioinfool20
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Comment: C: Easy way to run easily orthoMCL (Copy & paste)
... No. Do not delete the orthomcl database; you just need to flash the existing table from your first ran and then reconnect again to mysql. The instruction should be in the orthomcl manual. ...
written 7 months ago by bioinfool20
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Comment: C: Easy way to run easily orthoMCL (Copy & paste)
... Hi, it's kind off late but it means to me that there's incompatibility between the mysql and orthomcl you used. See in this link (https://www.biostars.org/p/293000/#318897) the orthomcl installation that works from above command. Good luck! ...
written 9 months ago by bioinfool20
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Comment: C: Showing FDR and log2FC in Volcano plot using R
... hi cpad0112, I would also like to draw a volcano map showing my diff expressed transcripts. But first, I want to filter my data from edgeRglm. After running edgreglm, i got logfc, logcpm, pval, & adjfdr val. I would like to log2 the logfc and logcpm values. How to do that? Or, is my logfc and ...
written 9 months ago by bioinfool20
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Comment: C: Volcano Plot from DEseq2
... Thanks for the quick reply. I used edgeR in getting my DE. Once I got them, I pre-filtered my DE list in excel. I only extract FDR<1e-5 which is my significant. Then from those list, my up-reg is log2FC>0 while my down is log2FC<0. I wanted to plot my FDR against log2FC. Can you embed th ...
written 10 months ago by bioinfool20
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Comment: C: Creating Interactive Volcano Plots with R and Plot.ly
... Hi Steve, Do you have the Rscript for this showing the up-and-down regulated transcripts using volcano? I already have pre-filtered data. My significant data is FDR<1e-5. My upregulated is log2FC>0 while my down is log2FC<0. ...
written 10 months ago by bioinfool20
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Comment: C: Volcano Plot from DEseq2
... Hi Kevin, I am wondering if you have rscript showing the upreguted and down regulated? Can you share them? ...
written 10 months ago by bioinfool20
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Comment: C: OrthoMCL installation on Ubuntu Linux
... Thanks for the link that provides a stepwise process for moving db with enough space. Apparently, I think the problem is that my disk is full in general. However, i cant delete programs or files as of the moment. I resolved with using other pc to complete the last remaining processes which i am sure ...
written 10 months ago by bioinfool20
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Comment: C: Error running OrthoMCL
... Doing df -h gives me tmpfs avail ~1.9G. In line with this, I am wondering if I can change the writing of the files from ***/tmp/MY40oycE*** to other folder? I had this folder with 613G available so I change the ***tmpdir*** of mysqld.cnf into its path. Apparently, when i restart mysql to take effect ...
written 10 months ago by bioinfool20
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Comment: C: Easy way to run easily orthoMCL (Copy & paste)
... This is going to be a lame question but how do i check the space of my hd? Anyway, I cant delete files as of the moment so I am wondering if I can change the writing of the file in other folder instead of `/tmp/MYza1d1c`? I had this folder with 613G, so I use this folder by writing its path in the ` ...
written 10 months ago by bioinfool20 • updated 3 months ago by RamRS21k

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