User: lshepard

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lshepard440
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Posts by lshepard

<prev • 84 results • page 2 of 9 • next >
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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 16 months ago by lshepard440
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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 16 months ago by lshepard440
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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 17 months ago by lshepard440
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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 17 months ago by lshepard440
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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 17 months ago by lshepard440
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Answer: A: Interpreting Bismark Methylation Extractor output
... It all depends on the options you used from Bismark. Here is the relevant information regarding your outputs from the docs: > Strand-specific methylation output files (default): As its default option, the bismark_methylation_extractor will produce a > strand-specific output which will use th ...
written 17 months ago by lshepard440
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Comment: C: ATAC-seq vs Bisulfite-sequencing
... Ok, by looking at the comment below, and with the fact that standard bisulfite will not be sufficient to differentiate between these two regulatory marks, I think your best bet is with ATAC-seq. ...
written 17 months ago by lshepard440
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Comment: C: Is Biostar Killing The Bioinformatics Core?
... Further, in the academic world, adding bioinformaticians as key personnel to grants is a big plus for grants that are NGS driven. In addition to a concise and well written methodology (which the bioinformatician can help), this will likely be seen as a well strategized research approach among review ...
written 17 months ago by lshepard440
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Comment: C: ATAC-seq vs Bisulfite-sequencing
... will your bisulfite sequencing be just standard bisulfite (where you can't differentiate 5mC vs 5hmC)? ...
written 17 months ago by lshepard440
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Comment: C: identify gene function
... You may consider functional annotation tools such as the one in [DAVID][1] where you can perform gene enrichment analysis and clustering. Other resources similar to DAVID are also available. If you want to look for functions of specific genes, then, most databases provides gene descriptions, and yo ...
written 17 months ago by lshepard440

Latest awards to lshepard

Great Question 10 months ago, created a question with more than 5,000 views. For Differential expression of scRNA-seq after Seurat
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
Scholar 16 months ago, created an answer that has been accepted. For A: which one is adapter and which one is index
Popular Question 16 months ago, created a question with more than 1,000 views. For Rsubread installation issues
Scholar 17 months ago, created an answer that has been accepted. For A: which one is adapter and which one is index
Popular Question 18 months ago, created a question with more than 1,000 views. For Rsubread installation issues
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Running STAR aligner with paired-end and single-end reads simultaneously
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Popular Question 2.2 years ago, created a question with more than 1,000 views. For Rsubread installation issues
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Rsubread installation issues
Scholar 2.8 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
Scholar 3.3 years ago, created an answer that has been accepted. For A: which one is adapter and which one is index
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