User: lshepard

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lshepard340
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Posts by lshepard

<prev • 77 results • page 1 of 8 • next >
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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 12 days ago by lshepard340
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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 12 days ago by lshepard340
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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 12 days ago by lshepard340 • updated 12 days ago by Emily_Ensembl18k
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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 13 days ago by lshepard340
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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 20 days ago by lshepard340
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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 25 days ago by lshepard340
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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 25 days ago by lshepard340
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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 25 days ago by lshepard340
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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 25 days ago by lshepard340
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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 26 days ago by lshepard340

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Scholar 13 days ago, created an answer that has been accepted. For A: which one is adapter and which one is index
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Scholar 18 months ago, created an answer that has been accepted. For A: which one is adapter and which one is index
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