User: Ashu

gravatar for Ashu
Ashu10
Reputation:
10
Status:
New User
Location:
San Diego
Last seen:
3 days, 9 hours ago
Joined:
5 years, 12 months ago
Email:
a************@gmail.com

Posts by Ashu

<prev • 14 results • page 1 of 2 • next >
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Comment: C: GenomicAlignments: Inverting strand when counting using summarizeOverlaps
... Dear Herve, I have the information that the RNA-Seq data I am working with is **single-end strand-specific**. I need to count reads on the reverse strand per gene, the gene names/position are in the GTF file and reads in the BAM file as shown below. Now, after researching many forums, tutorials a ...
written 19 days ago by Ashu10
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Answer: A: DiffBind: Error in heights * sapply(called, function(x) x)
... Hi Rory, It took me some time to get back on this, but here are the things you asked for: data <- DiffBind::dba(sampleSheet = samples, peakFormat="narrow", scoreCol = 5, filter = 20, config=data.frame(RunParallel=TRUE) ) SampleA-tNKT-liver-a Unknown None SampleA NONE 1 narrow SampleA-tNKT-live ...
written 6 months ago by Ashu10
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Comment: C: DiffBind: Error in heights * sapply(called, function(x) x)
... Hi Zhaolin, I ran into the same error message while running DiffBind. Did you happen to figure out the reason and/or a fix?  Thanks for your help! Ashu ...
written 7 months ago by Ashu10
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Comment: C: Need help with DESeq2's contrast feature
... I would still want to understand where could the interaction design be used, I will try to read more and find some examples.  Thanks for your help!   ...
written 9 months ago by Ashu10
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Comment: C: Need help with DESeq2's contrast feature
... Great thanks, I just ran the average method you described above and it seems to be picking genes that expect. Just for my understanding, would you be able to explain what is the difference between using interactions while doing the design as opposed to just using 4 groups? To be precise, what do th ...
written 9 months ago by Ashu10
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Comment: C: Need help with DESeq2's contrast feature
... Dear Michael, I would like to try the methods listed below and compare the results, but I don't know how to run DESeq2 for these, I just got confused when you listed so many methods before as I did not even know that DESeq2 can do all of that, may be that is why I sounded like asking for statistica ...
written 9 months ago by Ashu10 • updated 9 months ago by Michael Love24k
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Comment: C: Need help with DESeq2's contrast feature
... Completely understandable!  Not sure why bother asking me to create a new thread. Good day!! ...
written 9 months ago by Ashu10
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Comment: C: Need help with DESeq2's contrast feature
... Hi Michael, Not sure if you got my previous message! ...
written 9 months ago by Ashu10
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Comment: C: Need help with DESeq2's contrast feature
... The goal is to find differentially expressed genes in the group with diseased patients that have the MND condition as opposed to all others. I thought the average of all others would work but now I am unsure. I think I don't understand the right approach to consider to get those genes.     ...
written 9 months ago by Ashu10
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Comment: C: Using the "listValues" argument of DESEQ in multiple group comparisons
... Hi Michael, I just saw this, Thanks a lot for your reply, Here is the link to my new post: https://support.bioconductor.org/p/112346/ Thanks Ashu   ...
written 9 months ago by Ashu10

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