User: brismiller

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brismiller10
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10
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New User
Location:
Bellingham, WA, USA
Last seen:
13 minutes ago
Joined:
1 year, 3 months ago
Email:
b*********@gmail.com

Posts by brismiller

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Bowtie2: trying to implement position specific scoring options?
... Thanks h.mon this seems like the best option (CIGAR parsing)! I'll do a little more digging on how to do this and then post what I have found. Or if anyone else has done this before I would be happy to hear what they did. ...
written 5 days ago by brismiller10
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Bowtie2: trying to implement position specific scoring options?
... Hello all, Question: Is there a way to have bowtie2 give an alignment a score boost if specific regions of the read mapped perfectly? For example, say I have a 24nt read and I am using bowtie2 in –very-sensitive-local mode, if there is a match from positions 2-8 (from the 5' end of my read) I want ...
bowtie2 alignment score bowtie srna written 5 days ago by brismiller10
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GOstats Clarification: ontology information source
... Hey everybody, I am wondering what ontology file (.obo file) GOstats uses and where I could view it. Does GOstats pull its ontologies from geneontology.org (e.g. http://purl.obolibrary.org/obo/go.obo ) or is there some other source? I started looking at the source code but I haven't been able to pi ...
database ontology gostats go rna-seq written 6 weeks ago by brismiller10 • updated 6 weeks ago by Marks40
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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 10 weeks 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 10 weeks ago by brismiller10 • updated 10 weeks ago by EagleEye5.7k
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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 3 months ago by brismiller10 • updated 3 months 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 5 months ago by brismiller10 • updated 5 months ago by Kevin Blighe28k
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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 5 months ago by brismiller10 • updated 5 months ago by Kevin Blighe28k
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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 5 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 5 months ago by brismiller10 • updated 5 months ago by h.mon19k

Latest awards to brismiller

Supporter 5 months ago, voted at least 25 times.
Scholar 5 months ago, created an answer that has been accepted. For A: Program for updating custom annotations with new genome?

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