User: Fabio Marroni

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Fabio Marroni1.5k
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Posts by Fabio Marroni

<prev • 244 results • page 1 of 25 • next >
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Comment: C: WGCNA code for rna-seq data SFT plot issue
... > what kind of value ? The y values that you are plotting in the graph in which you are trying to plot the red line ...
written 10 days ago by Fabio Marroni1.5k
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Comment: C: WGCNA code for rna-seq data SFT plot issue
... Did you check that your values are not all larger (or smaller) than 0.8? Also, posting the plots would help ...
written 10 days ago by Fabio Marroni1.5k
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Answer: A: merging a number of overlapping sanger sequences
... I would suggest the suite [phred/phrap/consed][1]. It was widely used in the "old" Sanger days, and after all it was working pretty well. Consed is a "finishing" tool, which is nevertheless pretty useful to visualize assemblies and correct errors. The major drawback is that you might have to invest ...
written 24 days ago by Fabio Marroni1.5k
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Comment: C: Pop_Gen statistics from RNA SAM/BAM files
... Try [PopGenome][1] [1]: https://cran.r-project.org/web/packages/PopGenome/index.html ...
written 26 days ago by Fabio Marroni1.5k
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Comment: C: How to infer allele specific expression gene without phasing information?
... I gave a quick look to the paper, and it is true that they never mention haplotype phase. However, HapMap data is often phased. So, I don't know if they are implicitly using phased data. You are right. Theoretically, you need the phase to infer ASE. A quick and dirty approximation is to assume that ...
written 26 days ago by Fabio Marroni1.5k
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Comment: C: How can I go for RNA pooling of different tissues for Transcriptome Analysis?
... Hi, I am not sure in biostars is the best place to ask this question. This site is about bioinformatics. You might try asking the question on seqanswers or other forums related to molecular biology experiments. ...
written 26 days ago by Fabio Marroni1.5k
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Comment: C: Paired end sequencing with different read length: better to trim everything to a
... I agree with genomax. In addition, nobody prevents you from BOTH trimming read one to 66bp and using the R1 as 100bp single read and integrate the results, so that you get the most possible information. Finally... I am pretty sure that tools such as tophat-cufflinks (and probably the newer Hisat, as ...
written 26 days ago by Fabio Marroni1.5k
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Comment: C: How to perform KEGG pathway analysis in R?
... That's great, I didn't know... very useful if you are already using edgeR! ...
written 26 days ago by Fabio Marroni1.5k
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Answer: A: How to perform KEGG pathway analysis in R?
... I would suggest [KEGGprofile][1] or [KEGGrest][2] [1]: http://bioconductor.org/packages/release/bioc/html/KEGGprofile.html [2]: https://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html ...
written 27 days ago by Fabio Marroni1.5k
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Comment: C: Which of my mutations are SNPs? Is there an R package to annotate them?
... Some questions, so that people can help you better: 1) Isn't the type of variant specified in field 10 (Variant_Type) of a [MAF][1] file? 2) Can you post the first lines of the file? [1]: https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification#MutationAnnotationFor ...
written 4 weeks ago by Fabio Marroni1.5k

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Commentator 4 days ago, created a comment with at least 3 up-votes. For C: error in R
Scholar 26 days ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
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Scholar 3 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
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Scholar 19 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
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Teacher 22 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
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