User: Jacob Warner

gravatar for Jacob Warner
Jacob Warner550
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Website:
https://2-bitbio.com/
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@ScientistJake
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15 hours ago
Joined:
9 months, 3 weeks ago
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Posts by Jacob Warner

<prev • 87 results • page 1 of 9 • next >
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Comment: C: RNA-seq Co-expression network construction from the output of DESeq2
... No problem, try it a few ways. I found little difference between log2(x+1), rlog and varianceStabilizingTransformation when it came to the most highly connected genes. ...
written 15 hours ago by Jacob Warner550
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Answer: A: RNA-seq Co-expression network construction from the output of DESeq2
... Hi! [Point 4 in the WGCNA FAQ][1] addresses this: > We then recommend a variance-stabilizing transformation. For example, > package DESeq2 implements the function > varianceStabilizingTransformation which we have found useful, but one > could also start with normalized counts (or RPKM ...
written 16 hours ago by Jacob Warner550
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Comment: C: How do you find similar gene expression pattern to your GOI?
... Maybe you could cluster the data, then find which cluster your GOI is in. The other cluster members should have a similar profiles. A more complex way is to generate clusters using your input genes as initialization centroids. Although maybe somebody could give some insight because I have no exp ...
written 2 days ago by Jacob Warner550
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Comment: C: RShiny interactive volcano plots
... Assuming the rest of the app works you can use the `selectInput()` to change the data. It looks like the DE test is loaded at the `read.table` call? If that's true you can do: ui <- ... selectInput(inputId= 'DEtest', label='Pick a timepoint!', choices = c("3","7","24"...etc)) ... ...
written 5 days ago by Jacob Warner550
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Comment: C: trimming RNA-seq reads with adapter sequence?index? using trimmomatic
... I'm pretty sure the standard TruSeq3 adapter file will work, but to be sure you can look up your adapters [here][1] (page 18) and add them to a fasta file. I would include the universal and index adapter. [1]: https://support.illumina.com/content/dam/illumina-support/documents/documentation/che ...
written 7 days ago by Jacob Warner550
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Answer: A: trimming RNA-seq reads with adapter sequence?index? using trimmomatic
... Hello, I would recommend first running [fastqc][1] to first and check the over-represented sequences. The adapter contamination (and any other artifacts) should show up there. Then you can run trimmomatic tweaking the settings below: java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq ...
written 7 days ago by Jacob Warner550
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Comment: C: How to add GO pValue in blast2GO ?
... Perhaps you can use all the mapped GO terms as your background and the GO associated to DEGs to test for enrichment using a hypergeometric or fisher's exact test. But as Puli said you can use Revigo without p-values. ...
written 18 days ago by Jacob Warner550
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Answer: A: RSEM error: RSEM currently does not support gapped alignments, sorry!
... The error is pretty verbose. RSEM does not support gapped alignment. So when you map to a genome (which has introns) you need to use an end to end aligner like bowtie or set up STAR appropriately. Try these options for STAR to prohibit gaps: --alignEndsType EndToEnd --alignIntronMax 1 --alignIn ...
written 20 days ago by Jacob Warner550
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Comment: C: Time course experiment in RNASeq
... What is the format of your data? If it's raw count data you could use DEseq2 with time-series design. WIthout DE testing, uou can generate profiles like the one you linked by clustering the normalized count data. ...
written 21 days ago by Jacob Warner550
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Comment: C: UniProt ID mapping API call
... Have you looked at the flat files? Eg. http://www.uniprot.org/uniprot/Q9UM73.txt. Its especially easy to parse. It doesn't plug right in to your script there but you could set it up in a loop. ...
written 25 days ago by Jacob Warner550

Latest awards to Jacob Warner

Scholar 16 hours ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 9 weeks ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 10 weeks ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
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Teacher 5 months ago, created an answer with at least 3 up-votes. For A: 3D PCA issue
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Scholar 7 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 8 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data

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