User: Fabio Marroni

gravatar for Fabio Marroni
Fabio Marroni2.0k
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Italy
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http://www.fabiomarron...
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13 hours ago
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7 years, 8 months ago
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Posts by Fabio Marroni

<prev • 331 results • page 1 of 34 • next >
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Comment: C: How to merge read count of multiple sample in one fiel to be used for DESeq2 fol
... DESeq2 has several features for importing data: did you give a look to them? You can find them [here][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#input-data ...
written 14 hours ago by Fabio Marroni2.0k
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Comment: C: Exome Seq tutorial
... You might also give a look to answers to this question: https://www.biostars.org/p/363863/ ...
written 1 day ago by Fabio Marroni2.0k
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Comment: C: Genomics (DNA) Pipeline - Example
... A quick google search gave me these, I hope that they are useful! https://www.nature.com/articles/s41598-018-25022-6 http://bioinformatics.astate.edu/dna-pipeline/ https://genestack-user-tutorials.readthedocs.io/guide/intro-to-ngs.html ...
written 1 day ago by Fabio Marroni2.0k
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Comment: C: SNP Calling Parameter Settings
... > Actually, one human has no chance to carry so many SNPs. Why do you think so? What is the expected number of SNPs for one human subject on average? ...
written 22 days ago by Fabio Marroni2.0k
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Comment: C: Can't determine any relatedness using lcMLkin
... It would help if you posted the command you executed and the first lines of the output. Alternatively you can just mention what results you were expecting and what results you got. So, if some expert of the software is around can have a chance to understand what's going on. ...
written 22 days ago by Fabio Marroni2.0k
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Answer: A: Tajima's D Significant test
... You might look at the original paper form [Tajima][1], in which he published confidence limits of D at various significance levels. [1]: http://www.genetics.org/content/genetics/123/3/585.full.pdf ...
written 22 days ago by Fabio Marroni2.0k
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Comment: C: Hisat2 overall alignment rate below 50%
... Yes, blasting the unmapped reads sounds like the best option. However I cannot understand what do you mean by the "5 most common unmapped reads". Something like clustering together identical unmapped reads and counting how many times they occur in the read file? That's an interesting approach. ...
written 5 weeks ago by Fabio Marroni2.0k
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Answer: A: Should zero expression values be remove in eQTL analysis?
... No. I would only remove genes that have 0 levels of expression in a very large proportion of samples. More generally, you might want to filter genes with low variance across samples (see e.g. [this][1] paper, in the eQTL mapping paragraph of Materials and Methods section), since they are not info ...
written 6 weeks ago by Fabio Marroni2.0k
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Comment: C: Merging fastq files
... Using cat should work (see the comment by [RamRS][1]); I also recently used cat to merge fastq files without problems. However, as [Devon][2] correctly pointed out, if the fastq originates from different libraries, merging theme might not be a good idea. In that case you might want to insert the "r ...
written 6 weeks ago by Fabio Marroni2.0k
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Comment: C: Hisat2 overall alignment rate below 50%
... Some things you might check: 1) Did you use the same reference the authors used? 2) Did you find in the paper any statistics on read mapping? 3) Did you try blasting unmapped reads (or a large number of random reads) to nt or nr and see which organism they belong to? Maybe there is a large amount ...
written 6 weeks ago by Fabio Marroni2.0k

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Scholar 5 weeks ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 12 weeks ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Sample Sam File
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Appreciated 10 months ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 15 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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Commentator 16 months ago, created a comment with at least 3 up-votes. For C: error in R
Scholar 16 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 17 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 18 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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Scholar 2.9 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
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