User: sysboolean

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sysboolean50
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Systems Biologist

Posts by sysboolean

<prev • 13 results • page 1 of 2 • next >
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Answer: A: gene ID conversion
... A lot of researchers perform GO with human/mouse/zebrafish orthologs of their study organism's genes because those are species for which a significant amount of biological information is available. So I guess it is acceptable in your case too. However, when doing so, we assume that the orthologs are ...
written 6 days ago by sysboolean50
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Answer: A: low assignment reads % in RNA-seq
... Can you post more information about the origin of the samples ? Someone I know once performed RNA-seq on what they thought was human cell culture, but got poor alignment percents like yours. Further investigation (BLASTing a few reads against nr db) showed that the cells were from a non-human mammal ...
written 6 days ago by sysboolean50
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Comment: C: FASTQ level UMI correction for TCR analysis
... You can check fgbio toolkit, specifically the [Annotate BAM with UMIs][1] function. It is a command line toolkit that will add UMI information from a fastq to a BAM file. Tool description from its page: > Annotates existing BAM files with UMIs (Unique Molecular Indices, aka > Molecular IDs, M ...
written 6 days ago by sysboolean50
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Comment: C: Finding single-organism orthologs using NCBI Gene ID
... Hi Clement, thanks for the tips ! I will try this and come back to accept the answer when it works. ...
written 13 days ago by sysboolean50
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Answer: A: Comparing expression of genes within an RNA-seq Experiment to confirm pluripoten
... Have you thought about plotting the normalized count values on a [gene counts plot][1] ? If you have a list of genes (pluripotent markers & neuronal progenitor markers), you could make this plot for your list and check expression for each gene across conditions. [1]: http://www.bioconductor ...
written 14 days ago by sysboolean50
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Finding single-organism orthologs using NCBI Gene ID
... Hi all, I am reanalyzing a published RNA-seq dataset of a non-model organism (eel) and I have run into a roadblock regarding gene identifiers and finding orthologs. I generally use Ensembl biomart to find one2one orthologs between the query and target species (for eg: dog -> human/mouse), and t ...
ncbi orthologs rna-seq written 14 days ago by sysboolean50 • updated 13 days ago by clement.train30
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Comment: C: Removing variation identified by principal components in RNA-seq
... Oh that makes sense. I checked the results (p.adj < 0.05) and I have ~ 1100 genes that are significant for DE, but the log2FC range is only between -1.8 to +2.0. Thanks for helping me out ! ...
written 4 months ago by sysboolean50
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Comment: C: Removing variation identified by principal components in RNA-seq
... Thanks for the reply. So the differential expression result from DESeq2 is already corrected for the effect exerted by the subject ? How should I reconcile the DESeq2 results vs the PCA output ? ...
written 4 months ago by sysboolean50
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Removing variation identified by principal components in RNA-seq
... Hi all, I am a beginner with RNA-seq analysis, and using DESeq2. The experiment design is: cells from 4 subjects were cultured and then treated with a small molecule. I wish to perform DE between the control & treated conditions, while the subjects would be replicates. The formula I am using is ...
deseq2 rna-seq written 4 months ago by sysboolean50 • updated 4 months ago by swbarnes29.6k
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Comment: C: Pooled sequencing DNA barcode space and deconvolution
... Barcode deconvolution in this context is another way to say demultiplexing. In examples like the papers I linked, we need to solve a systems of equations to get the sample identity. I don't think deconvolution is a good term to use here as deconvolution has a specific meaning in mathematics. ...
written 9 months ago by sysboolean50

Latest awards to sysboolean

Scholar 9 months ago, created an answer that has been accepted. For A: Pooled sequencing DNA barcode space and deconvolution

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