User: Fabio Marroni

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Fabio Marroni1.6k
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Posts by Fabio Marroni

<prev • 259 results • page 1 of 26 • next >
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Comment: C: Help fixing my DGE heatmap?
... Try without decreasing=TRUE (you want the smaller p being the first one, not the last one). ...
written 1 day ago by Fabio Marroni1.6k
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Comment: C: Dot-ploting of two linkage maps in R
... Hi Matt, having the first three/four lines of the files would help. Maybe the two maps share the names/positions of the markers? However, I think it is easy. You do a scatter plot in which the X position is the position on your first file, and the Y is the position in the second file. Maybe I am m ...
written 1 day ago by Fabio Marroni1.6k
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Comment: C: best practices in trio snp and cnv analysis
... Bu maybe you can use plink. I suggest you give a look at the [old manual page][1] and then refer to the [new page][2] for downloading and having updated info. Also there are pipelines out: https://redmine.igm.cumc.columbia.edu/projects/biopipeline/wiki/Trio-Analysis_Pipeline Probably the pipeline ...
written 1 day ago by Fabio Marroni1.6k
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Comment: C: Bimodal GC curve in FASTQC for plant RNA-seq
... Also, we sometimes filter for chloroplast contaminants using [erne-filter][1]. This might be an option (I am never sure if for RNAseq one should filter for chloroplast or not. For DNAseq it helps a lot). However, I fully agree with genomax. If most of the reads are mapped to your target, then it is ...
written 1 day ago by Fabio Marroni1.6k
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Comment: C: Bimodal GC curve in FASTQC for plant RNA-seq
... maybe it is chloroplast? Or some other contaminant? ...
written 1 day ago by Fabio Marroni1.6k
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Comment: C: Help fixing my DGE heatmap?
... Which numbers are the first ten of "o"? Did you try to associate them to gene names? Which gene names were associated to them? Are those the same that you see in the heatmap? Since I am not an expert, it is really hard to help more by only looking at the code. ...
written 1 day ago by Fabio Marroni1.6k
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Answer: A: DeSEQ normalization for knockout
... The best option is to feed ALL of your raw counts to DESeq2 and normalize all the data together. DESeq2 (and if I well remember DESeq as well) has options to perform analysis when you have more than two levels (treated and control). You can find some mention of it at the paragraph "Contrasts" of the ...
written 3 days ago by Fabio Marroni1.6k
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Answer: A: Cummerbund Isn'T Managing Cuffdiff Database
... Just to summarize things. Please, correct me if I miss something. In the gene_exp.diff file (and in all the .diff files) there are two columns called sample_1 and sample_2, respectively. These are the sample names (for @mad.cichlids). These columns SHOULD NOT 1) assume the "T" value (@Conana experi ...
written 20 days ago by Fabio Marroni1.6k
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Comment: C: GO enrichment analysis using R
... I am sorry, I didn't try the module you are mentioning... maybe you might ask help to the authors? ...
written 24 days ago by Fabio Marroni1.6k
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Comment: C: Haplotype LD block without genotypes
... Given that LD is the non-random association of alleles at different loci, I would say: NO! However, if you are working in human and you have a list of SNPs, maybe you can browse the 1000 genome data and see if they share haplotype blocks data (I think they do, but I do not know where). ...
written 4 weeks ago by Fabio Marroni1.6k

Latest awards to Fabio Marroni

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 5 weeks ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: error in R
Scholar 11 weeks ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Scholar 12 weeks ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 4 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
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Scholar 5 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 21 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Scholar 21 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 2.0 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
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