User: datascientist28

gravatar for datascientist28
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University of Washington
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Posts by datascientist28

<prev • 73 results • page 1 of 8 • next >
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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 19 days ago by datascientist28320
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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 3 months ago by datascientist28320
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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 3 months ago by datascientist28320
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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 3 months ago by datascientist28320
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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 3 months ago by datascientist28320
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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 3 months ago by datascientist28320
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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 3 months ago by datascientist28320
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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 3 months ago by datascientist28320
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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 3 months ago by datascientist28320
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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 9 months ago by datascientist28320

Latest awards to datascientist28

Student 9 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 13 months ago, created a question with more than 1,000 views. For Help understanding MACS2 --extsize and --shift
Popular Question 13 months ago, created a question with more than 1,000 views. For Help understanding MACS2 --extsize and --shift
Popular Question 14 months ago, created a question with more than 1,000 views. For Trim Galore Bug?
Popular Question 15 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 15 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 15 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 18 months ago, voted at least 25 times.
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: ATAC Mapping rate
Scholar 18 months ago, created an answer that has been accepted. For A: ATAC Mapping rate
Student 19 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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