User: bioinfool

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bioinfool20
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Posts by bioinfool

<prev • 27 results • page 1 of 3 • next >
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Comment: C: How To Filter Mapped Reads With Samtools
... What if I only want to keep the mapped reads and remove all the unmapped? What should I do? Given that the unmapped is already deleted, to to convert the bam file into a fastq file then? ...
written 9 days ago by bioinfool20
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Comment: C: Volcano plot help code
... tried installing the package but it says > Warning in install.packages: package 'EnhancedVolcano' is not available (for R ver 3.5.3) what to do? ...
written 5 months ago by bioinfool20
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Comment: C: Volcano plot help code
... thanks for the quick reply. i am fairly new to this so i had difficulty understanding how things work here. anyway, yes, i already have my DE data, which i already filtered. it consist of my_transcript_name, log2FC, & FDR value. since my data is already filtered, i just wanted to plot it using v ...
written 5 months ago by bioinfool20
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Comment: C: Volcano plot help code
... kevin, this tool is very good in providing beautiful figure. but your script use airway dataset, right? but i got confused with the series of replies. can you redirect me to the newer ver so i can follow it using my data? ...
written 5 months ago by bioinfool20
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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 7 months 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 13 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 15 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 15 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 16 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 16 months ago by bioinfool20

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