User: olechnwin

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olechnwin20
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3 years, 5 months ago
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t*******@osu.edu

Posts by olechnwin

<prev • 35 results • page 1 of 4 • next >
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Comment: C: Diffbind: an error when generating DBA lies
... Thanks for posting about file location not correct. That's helpful! ...
written 8 weeks ago by olechnwin20
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cutoff for expressed genes in DESeq2
... Hello, I've analyzed my RNA-seq data using DESeq2 and now I am trying to see whether some gene of interest are expressed in our dataset. I found this [paper][1] which uses RPKM cut off of 0.3 to defined genes as expressed. I found out that I can use the fpkm function in DESeq2 to convert the counts ...
deseq rna-seq written 4 months ago by olechnwin20 • updated 4 months ago by swbarnes27.4k
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Comment: C: maker has been running for a long time
... Sadly, I'm still not approved. I've sent two requests. I tried running their example_01_basic using hsap_contig.fasta genome and it has been running for 20+ hours. I wonder if you have tried running their example? how long does it take? I'm running this example using mpi with 4 processes. This is ...
written 6 months ago by olechnwin20
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Comment: C: maker has been running for a long time
... Hi, Thank you for taking the time to comment. I'm using MAKER in centOS Linux. I'll try to post in the google group too. I'm waiting for them to approve my subscription. ...
written 6 months ago by olechnwin20
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maker has been running for a long time
... Hi all, I am running genome annotation using MAKER. It's a human genome so about ~3Gb but with ~ 3500 contigs. I am running MAKER with 20 processes (mpich). It's been running for 4 days on the same 19 contigs. I cannot tell whether it is supposed to be this long or whether it is stuck on somethi ...
genome annotation maker written 6 months ago by olechnwin20
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Answer: A: Repeat Modeler keeps failing
... I'm leaving this here, it maybe useful for someone. I was able to fix the error above by re-installing and re-configuring RepeatModeler. Which includes re-installing and re-configuring RepeatMasker. Most importantly I think I did not configure the RepeatMasker library correctly. This is the log on ...
written 6 months ago by olechnwin20
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Repeat Modeler keeps failing
... I really hope someone can help me with this. I've been trying to run repeatmodeler on my denovo assembled human cell line genome. It ran for ~ 11 days then failed. It ran RepeatModeler to round #5. The following is part of the log before it failed: RepeatModeler Round # 5 ================== ...
eleredef recon repeatmodeler written 7 months ago by olechnwin20
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Comment: C: Interpretation of several pairwise overlaps
... These are just gene names overlap. For example: gom.obj["H3K9me3", "Exp Medium"] GeneOverlap object: listA size=297 listB size=6011 Intersection size=142 Overlapping p-value=7.1e-13 the background gene size is the same for all the pairwise overlap tests. ...
written 8 months ago by olechnwin20
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Interpretation of several pairwise overlaps
... The following were taken from an example in GeneOverlap library where it did 12 pairwise gene overlap tests using Fisher test. re-producible code: library(GeneOverlap) data(GeneOverlap) gom.obj <- newGOM(hESC.ChIPSeq.list, hESC.RNASeq.list, gs.RNASeq) draw ...
fisher test R geneoverlap statistics written 8 months ago by olechnwin20 • updated 8 months ago by predeus1.3k
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Comment: C: align Falcon-unzip contigs to itself using minimap
... This is unrelated but I remember yesterday there was only a button to upvote. There was no button to accept. What did you do? ...
written 10 months ago by olechnwin20

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Popular Question 4 months ago, created a question with more than 1,000 views. For Recommend tools to Identify splice site regulatory elements
Popular Question 22 months ago, created a question with more than 1,000 views. For macs2: how to retrieve normalized counts

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