User: olechnwin

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olechnwin30
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3 days, 2 hours ago
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4 years, 5 months ago
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t*******@osu.edu

Posts by olechnwin

<prev • 41 results • page 1 of 5 • next >
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Comment: C: trim_galore: Unable to create directory File exists
... I've been getting consistently no error when I run the script without specifying the output directory. It seems to be the answer for now. I'll wait until I've ran several more samples to be sure the error doesn't happen again. ...
written 6 weeks ago by olechnwin30
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Comment: C: trim_galore: Unable to create directory File exists
... Thanks for your reply. That's what I thought at first that it failed because trim directory already exist. However, trim_galore was ran for 20 paired fastq files and it will randomly fail for some but not all of them. So, it tries to create trim directory every time and and no error for the other p ...
written 6 weeks ago by olechnwin30
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trim_galore: Unable to create directory File exists
... Hi All, I'm hoping someone can help me. I'm running trim_galore in a pipeline to automate trimming multiple fastq files. It works for some paired fastq files but then failed with "`Unable to create directory File exists`". This is the code I ran `trim_galore`: trim_galore -q 20 --length 20 -- ...
next-gen chip-seq trim_galore rna-seq written 6 weeks ago by olechnwin30
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Comment: C: CSAW- functions not present
... Hi Francesca, I was puzzled that some functions were not automatically installed either. But, as ATpoint pointed out, this was because I was viewing the latest manual but then installed a different version of csaw. I was not thinking about version difference as I recently just installed csaw. Howev ...
written 11 months ago by olechnwin30
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Comment: C: IDR (Irreproducible Discover Rate) on more than two replicates
... Appreciate your insights on replicates even if you didn't answer the actual question :-). I noticed how variable is the ChIP, that's why I'm trying to utilize IDR to help with this. ...
written 11 months ago by olechnwin30
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IDR (Irreproducible Discover Rate) on more than two replicates
... Hi, Can someone share their experience on using IDR on more than two replicates? I know Encode pipeline can do this but it's really hard for me to see how they do this. Or if someone can point me to the script used for Encode for more than two replicates that would be great too. Thank you in advan ...
replicates chip-seq idr peak-calling written 11 months ago by olechnwin30 • updated 11 months ago by zhuobaowen10
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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 14 months ago by olechnwin30
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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 16 months ago by olechnwin30 • updated 16 months ago by swbarnes29.6k
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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 19 months ago by olechnwin30
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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 19 months ago by olechnwin30

Latest awards to olechnwin

Popular Question 25 days ago, created a question with more than 1,000 views. For Recommend tools to Identify splice site regulatory elements
Popular Question 11 months ago, created a question with more than 1,000 views. For Recommend tools to Identify splice site regulatory elements
Popular Question 16 months ago, created a question with more than 1,000 views. For Recommend tools to Identify splice site regulatory elements
Popular Question 2.9 years ago, created a question with more than 1,000 views. For macs2: how to retrieve normalized counts

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