Moderator: Benn

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Benn7.9k
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Posts by Benn

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Comment: C: Deferentially Expressed Genes Heatmap
... Your question is very general, my advice is to find some tutorials on Google and try them first. Then if you run into some problems, come back here with a more specific question and share your code thus far. Good luck. ...
written 4 months ago by Benn7.9k
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Comment: C: Hi, I have 19 RNAseq data(9 control,10 cancer) with CSV format and i want to per
... Try to read the DEseq manual first please, if you run into something specific doing that you can ask here for help. Your question now is too general. ...
written 4 months ago by Benn7.9k
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Answer: A: Calculating Pairwise Alignment Scores
... Gap opening penalty, is the number of points you'll have to subtract when a gap starts (12 in your case with blosum62), and extension penalty is when the gap extents further after opening (so each additional gap after the first opening one). When a gap closes and a new gap opens, you'll get a new o ...
written 4 months ago by Benn7.9k
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Comment: C: cant find output after featureCounts
... I have never used the program in R, but I think your reads counts table will be saved in R object `newcount`. Can you check that object with e.g. head? head(newcount) ...
written 4 months ago by Benn7.9k
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Answer: C: Potential post-doc PI giving exam as part of hiring process
... I think you are right, this is not normal. I think the PI is somewhat overzealous and too enthusiastic, and doesn't realize the time and effort you'll have to spend in this little exam. I think you made the right decision with rejecting the offer. When I had job interviews, sometimes I got the "exam ...
written 5 months ago by Benn7.9k
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Answer: A: Deferentially Expressed Genes using Genes count data obtained from RNASeq
... A good way to start is reading the manual of [limma][1]. Read about the RNA-seq methods and follow some of the case studies. Good luck. [1]: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf ...
written 5 months ago by Benn7.9k
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Comment: C: Enriched GO terms not present in background annotation: BLAST2GO
... How did you do enrichment, with which package? It might be that your BLAST2GO annotation is older than the GO database that was used for enrichment analysis. The GO database is very dynamic and changes with every update. So please explain more about how you did the enrichment analysis. ...
written 6 months ago by Benn7.9k
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Answer: A: Single-color and two color Agilent array analyzing in R
... Two-channel (color) microarrays are usually normalized with LOESS, but one-channel arrays usually only with a between-array method (like quantile). The best tool to use is [limma][1], you can read in the manual how to normalize and analyze these different array types, including case studies with scr ...
written 6 months ago by Benn7.9k
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Answer: A: How to do a GO enrichment analysis for large amount of data using R
... To do GO enrichment analysis for more groups in parallel you can try [clusterProfiler][1]. I used it once to do GO enrichment analysis for 6-7 groups simultaneously. [1]: https://bioconductor.org/packages/release/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html ...
written 6 months ago by Benn7.9k
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Comment: C: How to normalize my rna seq data?
... You could use [voom][1] normalization from limma, and add the quantile normalization in there with argument `normalize.method = "quantile"`. However, start with real counts, derived from featureCounts instead of RSEM. [1]: https://www.rdocumentation.org/packages/limma/versions/3.28.14/topics/voo ...
written 6 months ago by Benn7.9k

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Popular Question 11 weeks ago, created a question with more than 1,000 views. For phred 33 from Ion S5?
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Scholar 7 months ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: trimming the paired end reads with cutadapt
Scholar 11 months ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
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