User: datascientist28

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University of Washington
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Posts by datascientist28

<prev • 75 results • page 1 of 8 • next >
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Answer: A: HISAT2-build killed: 9 macos
... It was a memory issue because -ss and --exon require 200GB of memory. Removing those flags caused it to work. ...
written 10 weeks ago by datascientist28350
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HISAT2-build killed: 9 macOS
... I'm getting the most random error on my genome build the output is killer 9, i've seen very conflicting reports on stackexchange and the goggles, does anyone have advice on what this means and how i can fix or look into this?? It outputs .ht2 files but is missing some of them. It only outputs the 1 ...
hisat2 build rna-seq index written 10 weeks ago by datascientist28350
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Comment: C: For Mean Expression/FC Calculations in scRNA-seq, should I use All cells or only
... Monocle runs something similar to DEseq but doesn't have a results() function (of DESeq) that calculates that. I already have a normalized counts table, as I said above, and since I'm running through the program, I of course quality filter already. I'm just wondering the question of which cells to u ...
written 7 months ago by datascientist28350
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Comment: C: Naive BASH question on top to bottom programming regarding my alignment script
... Reason I thought that was because Sample2 tmp merge files were being made before Sample1 was merged and got a memory error ...
written 10 months ago by datascientist28350
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Comment: C: Naive BASH question on top to bottom programming regarding my alignment script
... Got it. Sorry for the confusion and not saying everything in my original post ...
written 10 months ago by datascientist28350
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Comment: C: Naive BASH question on top to bottom programming regarding my alignment script
... I added a comment to Jean's answer? Does this bg have this effect? ...
written 10 months ago by datascientist28350
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Comment: C: Naive BASH question on top to bottom programming regarding my alignment script
... Oh this is a good point. I did start the command and then put it in the background by control-z and `bg`, would that have an effect?? ...
written 10 months ago by datascientist28350
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Comment: C: Naive BASH question on top to bottom programming regarding my alignment script
... Wow learn something new about bash everyday. Thanks for the input ...
written 10 months ago by datascientist28350
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Naive BASH question on top to bottom programming regarding my alignment script
... I'm confused as to why the two bowtie lines are running at the same time? I was under the impression that everything in unix is run top to bottom and the second bowtie line wouldn't start running until the first is completed. The reason I ask is these commands are running simultaneously and I'm havi ...
unix bash written 10 months ago by datascientist28350
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Comment: C: What are the best tools for differential detection between ATAC-seq samples?
... Aka more biological noise in signal than ChIP data ...
written 10 months ago by datascientist28350

Latest awards to datascientist28

Scholar 10 weeks ago, created an answer that has been accepted. For A: ATAC Mapping rate
Great Question 7 months ago, created a question with more than 5,000 views. For What are the best tools for differential detection between ATAC-seq samples?
Popular Question 7 months ago, created a question with more than 1,000 views. For Bowtie Parameter Switch Error
Student 7 months ago, asked a question with at least 3 up-votes. For What are the best tools for differential detection between ATAC-seq samples?
Student 16 months ago, asked a question with at least 3 up-votes. For What are the best tools for differential detection between ATAC-seq samples?
Popular Question 19 months ago, created a question with more than 1,000 views. For Help understanding MACS2 --extsize and --shift
Popular Question 20 months ago, created a question with more than 1,000 views. For Help understanding MACS2 --extsize and --shift
Popular Question 21 months ago, created a question with more than 1,000 views. For Trim Galore Bug?
Popular Question 21 months ago, created a question with more than 1,000 views. For What is the reason for trimming reads to 30 bp for ATAC-seq aligning?
Appreciated 22 months ago, created a post with more than 5 votes. For What is the reason for trimming reads to 30 bp for ATAC-seq aligning?
Good Question 22 months ago, asked a question that was upvoted at least 5 times. For What is the reason for trimming reads to 30 bp for ATAC-seq aligning?
Supporter 2.0 years ago, voted at least 25 times.
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: ATAC Mapping rate
Scholar 2.1 years ago, created an answer that has been accepted. For A: ATAC Mapping rate
Student 2.2 years ago, asked a question with at least 3 up-votes. For What is the reason for trimming reads to 30 bp for ATAC-seq aligning?

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