User: Fabio Marroni
Fabio Marroni • 2.0k
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Posts by Fabio Marroni
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... 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 Marroni • 2.0k
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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 Marroni • 2.0k
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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 Marroni • 2.0k
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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 Marroni • 2.0k
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... 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 Marroni • 2.0k
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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 Marroni • 2.0k
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... 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 Marroni • 2.0k
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... 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 Marroni • 2.0k
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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 Marroni • 2.0k
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... 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 Marroni • 2.0k
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