User: lshepard

gravatar for lshepard
lshepard400
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Posts by lshepard

<prev • 79 results • page 1 of 8 • next >
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Comment: C: Difference between annotation from Ensembl and UCSC.
... Indeed, but be aware that there are minor differences in chromosomal coordinates between Ensembl and UCSC (e.g.: if someone uses Ensembl genome + annotation, this will be 1bp off from UCSC genome + UCSC annotation. Importantly, when I mention UCSC annotation, this goes for all the annotation UCSC ho ...
written 6 months ago by lshepard400
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Comment: C: To generate an scRNA counts file using barcodes.tsv, genes.tsv and matrix.mtx fi
... No, Seurat does not require the data to be in csv. Use `Read10X` to import your 10X data for object creation. ...
written 9 months ago by lshepard400
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Comment: C: Promoter in gene body region of another gene - feedback on definition or consens
... Very true Kevin, thank you for that additional thought and thank you Devon. ...
written 11 months ago by lshepard400
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Comment: C: Promoter in gene body region of another gene - feedback on definition or consens
... Emily, thank you so much for this reply, and all the work from Ensembl. This helps me greatly. ...
written 11 months ago by lshepard400
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Promoter in gene body region of another gene - feedback on definition or consensus
... Hi everyone, I am wondering if there is a standard/consensus about how we ***should*** define promoter regions which may fall upon gene body regions of another gene. To expand: say I define a promoter as 1000 bp away from the TSS and I want to intersect CpG methylation to find regulatory regions (g ...
annotation written 11 months ago by lshepard400 • updated 11 months ago by Emily_Ensembl20k
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Comment: C: How to merge Kallisto TSV files for use with Tximport
... Do you intend on using DESeq2 afterwards? If so, one potential option you can explore is the `collapseReplicates` function of DESeq2. I know this is not the direct answer here since it is after the usage of tximport, but just an FYI for you to explore. Alternatively, why did you not merge these earl ...
written 11 months ago by lshepard400
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Answer: A: DESeq2 lfc shrinkage
... It has been a while but I just saw this. To not leave it unanswered in case others come across this: check the potential coefficients from using the function `resultsNames(dds)` [`dds`: object name to `DESeqDataSet`] Further, check the section of the vignette called "Note on factor levels", to chan ...
written 11 months ago by lshepard400
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Comment: C: Interpreting Bismark Methylation Extractor output
... Did you read the comment I left you? I added this information to my original reply shortly after posting to make things easier ..., please read the answer in full if you would like assistance... (and again below) > Regarding non CG context, refer to the "Context-dependent methylation output file ...
written 12 months ago by lshepard400
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Comment: C: Interpreting Bismark Methylation Extractor output
... Also, as an FYI, don't post a comment to your own question in the answer section of this forum. Just add it to the `ADD COMMENT` section. ...
written 12 months ago by lshepard400
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Comment: C: Interpreting Bismark Methylation Extractor output
... Yes, look at my last paragraph, I even added an edit shortly after posting it to make things clear. ...
written 12 months ago by lshepard400

Latest awards to lshepard

Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Running STAR aligner with paired-end and single-end reads simultaneously
Scholar 11 months ago, created an answer that has been accepted. For A: which one is adapter and which one is index
Popular Question 12 months ago, created a question with more than 1,000 views. For Rsubread installation issues
Scholar 12 months ago, created an answer that has been accepted. For A: which one is adapter and which one is index
Popular Question 13 months ago, created a question with more than 1,000 views. For Rsubread installation issues
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Running STAR aligner with paired-end and single-end reads simultaneously
Supporter 14 months ago, voted at least 25 times.
Popular Question 22 months ago, created a question with more than 1,000 views. For Rsubread installation issues
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Rsubread installation issues
Scholar 2.4 years ago, created an answer that has been accepted. For A: which one is adapter and which one is index
Scholar 2.5 years ago, created an answer that has been accepted. For A: which one is adapter and which one is index
Scholar 2.9 years ago, created an answer that has been accepted. For A: which one is adapter and which one is index
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: which one is adapter and which one is index
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Rsubread installation issues

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