User: datascientist28

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University of Washington
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Posts by datascientist28

<prev • 64 results • page 1 of 7 • next >
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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 3 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 4 months ago by datascientist28300
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Comment: C: What are the best tools for differential detection between ATAC-seq samples?
... So I started to draft up a response and then thought it might just be easier to send the data. I'll provide a link to a correlation heat map and MDS plot from edgeR. The problem that we have had with our data is that our sequencing depth has varied pretty substantially so this could have some affect ...
written 5 months ago by datascientist28300
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Comment: C: What are the best tools for differential detection between ATAC-seq samples?
... Is there normally a lot of variability in your data? When I do a spearman rank correlation, all of my samples are not very well related to eachother (spearman < 0.5) but the peaks look good among replicates. Is this abnormal? ...
written 5 months ago by datascientist28300
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Comment: C: Meta-Analysis chip-seq data
... No one is gonna answer your question correctly if you use a vague term. Meta literally means anything. ...
written 5 months ago by datascientist28300
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Comment: C: What are the best tools for differential detection between ATAC-seq samples?
... I use featurecounts from Rsubread, a bioconductor package. There is a pretty good example on pages 5-7 of the vingette under Section 3 "Counting mapped reads for genomic features". You can also do this via HTSeq-count. ...
written 6 months ago by datascientist28300
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Filter by multiple columns above count threshold in R
... So I'm having a brain cramp and I think I'm over thinking it. I'm doing an RNA-seq experiment and want to filter my counts table by if at least four columns have above 20 counts. Any clue how to do this? The function I wrote takes way too long and there has got to be an easier way. ...
workflow rna-seq written 7 months ago by datascientist28300 • updated 7 months ago by Michael Dondrup43k
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Comment: C: Python VCF parser
... https://www.google.com/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=python+vcf+parser&* ...
written 8 months ago by datascientist28300
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Answer: A: Long Read Length, yet STAR says many reads too short
... I had a similar problem a couple months ago. It's poorly labeled, too short doesn't actually mean literally "too short". "too short" means that the best alignments STAR found were too short to pass the filters. This is controlled by --outFilterScoreMinOverLread --outFilterMatchNminOverLread whic ...
written 8 months ago by datascientist28300
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Comment: C: Chip-seq on pooled replicates
... Yeah it seems that the noise in a sample could be adding to this. ...
written 9 months ago by datascientist28300

Latest awards to datascientist28

Popular Question 7 months ago, created a question with more than 1,000 views. For Help understanding MACS2 --extsize and --shift
Popular Question 7 months ago, created a question with more than 1,000 views. For Help understanding MACS2 --extsize and --shift
Popular Question 8 months ago, created a question with more than 1,000 views. For Trim Galore Bug?
Popular Question 8 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 9 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 9 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 12 months ago, voted at least 25 times.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: ATAC Mapping rate
Scholar 12 months ago, created an answer that has been accepted. For A: ATAC Mapping rate
Student 13 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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