User: brismiller

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brismiller10
Reputation:
10
Status:
New User
Location:
Bellingham, WA, USA
Last seen:
3 days, 2 hours ago
Joined:
1 year ago
Email:
b*********@gmail.com

Posts by brismiller

<prev • 14 results • page 1 of 2 • next >
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Comment: C: GO Analysis Clarification using GOstats using hyperGTest()
... Yes, there is no Tetrahymena specific file, but the file used to generate the universe for my analysis was downloaded from the [geneontology.org's annotation download page][1] with the filter "+ taxon_subset_closure_label: Tetrahymena thermophila SB210" to download all 34679 Tetrahymena annotations. ...
written 6 days ago by brismiller10
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GO Analysis Clarification using GOstats using hyperGTest()
... Hey everybody, I have a question about how the hyperGTest() works with regard to the GO terms tested. From one of my results tables, some of the GO terms returned are not in my GO universe (the GO term is not in my organism's obo file). For example, this GO term was shown to be significantly enri ...
gene ontology rna-seq go written 7 days ago by brismiller10 • updated 6 days ago by EagleEye5.5k
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Decreased base quality at start of RNA seq reads
... Hey all, While running quality control steps for an RNA-Seq experiment I can see a decrease in the read quality score at the first few nucleotides (see below). ![enter image description here][1] I read the fastQC manual and it said on the Per [Base Sequence Quality][2] that poor quality at the sta ...
base quality position rna-seq sequencing written 7 weeks ago by brismiller10 • updated 7 weeks ago by Wietje150
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Clarification on how DSEeq2 Dispersion Curve is Generated
... Hi everyone, I have a clarification question on how the average expression versus dispersion curve is generated. From the paper, it says that Deseq2 uses 'all samples' in making the plot, but is that all samples for a given sample type (genotype) or is it all samples regardless of genotype? I am ...
gene correction deseq2 dispersion rna-seq written 12 weeks ago by brismiller10 • updated 12 weeks ago by Kevin Blighe24k
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RNAseq sva-seq drops number of DE genes?
... Hey everybody, I have a question about the Surrogate Variables Analysis(SVA) implementation. I have an RNA-seq dataset counts matrix that I am piping into DESeq2 to identify differentially expressed genes. When the RNA libraries were prepared the cells were grown in batches with one wild-type strai ...
R sva svaseq rna-seq written 3 months ago by brismiller10 • updated 3 months ago by Kevin Blighe24k
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Comment: C: Alignment and Counting strandedness redundancy?
... Thank you h.mom this answers my question! For my own sanity, I made sure that the two sample aligned with "F" or "R" had the same number of reads with the 16 flag (for read being on the reverse strand). They were the same as anticipated. #sam made using --rna-strandness "R" samtools view - ...
written 3 months ago by brismiller10
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Alignment and Counting strandedness redundancy?
... Hi everyone I have a question about the parameters to use for my SE RNA-Seq samples for the alignment and counting steps of my pipeline. I am using hisat2 and featureCounts for the alignment and counting programs, upstream of DESEQ2 for detecting differential expression. I know that my reads are re ...
alignment featurecounts rna-seq strand hisat2 written 3 months ago by brismiller10 • updated 3 months ago by h.mon16k
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Answer: A: Program for updating custom annotations with new genome?
... In the end, I just manually used BLAST to find the new coordinates. For each annotation I extracted the sequence from both genomes and compared them, most were the same (unchanged coordinates), and there were only 20 that I had to BLAST. This question is resolved, but if people want to comment on wh ...
written 3 months ago by brismiller10
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Comment: C: Program for updating custom annotations with new genome?
... Correct we are not talking about 'normal protein coding'. In fact, they are not genes at all, they are sRNA precursor ranges (from which sRNA are produced). From the answer below I saw that there were 10 annotations that resulted in a new sequence in the new genome. For some of them the strandednes ...
written 3 months ago by brismiller10
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Comment: C: Program for updating custom annotations with new genome?
... Thanks for this suggestion, I will keep this in mind if I need to work with a larger annotation set. ...
written 3 months ago by brismiller10

Latest awards to brismiller

Supporter 3 months ago, voted at least 25 times.
Scholar 3 months ago, created an answer that has been accepted. For A: Program for updating custom annotations with new genome?

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