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 3 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 6 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 6 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 6 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 6 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 6 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 6 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 6 months ago by datascientist28350
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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 6 months ago by datascientist28350
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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 12 months ago by datascientist28350

Latest awards to datascientist28

Student 12 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 15 months ago, created a question with more than 1,000 views. For Help understanding MACS2 --extsize and --shift
Popular Question 16 months ago, created a question with more than 1,000 views. For Help understanding MACS2 --extsize and --shift
Popular Question 17 months ago, created a question with more than 1,000 views. For Trim Galore Bug?
Popular Question 17 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 18 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 18 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 20 months ago, voted at least 25 times.
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: ATAC Mapping rate
Scholar 21 months ago, created an answer that has been accepted. For A: ATAC Mapping rate
Student 22 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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