User: datascientist28

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University of Washington
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Posts by datascientist28

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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 7 days ago by datascientist28300
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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 7 days ago by datascientist28300
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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 7 days ago by datascientist28300
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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 7 days ago by datascientist28300
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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 8 days ago by datascientist28300
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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 8 days ago by datascientist28300
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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 8 days ago by datascientist28300
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Comment: C: What are the best tools for differential detection between ATAC-seq samples?
... I used to use diffReps for ChIP data and I thought I could apply it to ATAC when starting out but it did not work very well for me. I think because ATAC data tends to be much more noisy than ChIP ...
written 8 days ago by datascientist28300
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Comment: C: Help understanding MACS2 --extsize and --shift
... No it's the extension size that it will extend the reads to for smoothing the pileup ...
written 6 months ago by datascientist28300
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Does read counts for ATAC-seq differential detection make sense?
... So I've been following a pipeline recommended to me on this discussion section. (https://www.biostars.org/p/224440/#258171). A post doc in my lab brought up an argument about his tentativeness to use counts. I don't have a great answer for this. Can someone help us understand this better? his 'pro ...
atac-seq edger differential accessibility written 7 months ago by datascientist28300

Latest awards to datascientist28

Student 6 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 9 months ago, created a question with more than 1,000 views. For Help understanding MACS2 --extsize and --shift
Popular Question 10 months ago, created a question with more than 1,000 views. For Help understanding MACS2 --extsize and --shift
Popular Question 11 months ago, created a question with more than 1,000 views. For Trim Galore Bug?
Popular Question 11 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 12 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 12 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?
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Teacher 15 months ago, created an answer with at least 3 up-votes. For A: ATAC Mapping rate
Scholar 15 months ago, created an answer that has been accepted. For A: ATAC Mapping rate
Student 16 months 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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