User: elcortegano
elcortegano • 50
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Posts by elcortegano
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... For the intergenic regions GFF file, I had to remove the middle '0' when creating chromSizes.bed so it's a genome file. Other than that, works like a charm. ...
written 8 weeks ago by
elcortegano • 50
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199
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... You have to use single quotation ('') inside awk brackets:
grep -v ^# my.cmscan.tblout | awk {' printf(“%s\tinfernal\t%s\t%s\t%s\t%s\t%s\t.\n”, $4, $2, $10, $11, $17, $12); '} > my.cmscan.gff ...
written 3 months ago by
elcortegano • 50
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... Thank you for the solution, and for the advice! ...
written 3 months ago by
elcortegano • 50
0
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1
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230
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1
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... Yes, I get the same output ...
written 3 months ago by
elcortegano • 50
0
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1
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230
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... I just updated to biomaRt 2.44, but the same error remains. Wonder why that different errors ...
written 3 months ago by
elcortegano • 50
10
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1
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230
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6 follow
1
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... I'm trying to give it a look at the phytozome database in biomart, but just as I want to explore a list of known loci, the program returns an error message related to biomaRt webservice. I have tried changing the Mart from phytozome to ensembl, and seems to be related to that. However, I don't see h ...
written 3 months ago by
elcortegano • 50
• updated
3 months ago by
Mike Smith • 1.5k
1
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95
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... Hi, I'm trying to use [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html) for dN/dS computation, but I am failing at the very beggining trying to compile the software for Manjaro Linux (kernel 4.19.125-1-MANJARO).
I am downloading the latest package (named `paml4.9j.tgz`), and following steps i ...
written 3 months ago by
elcortegano • 50
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... According to [VCF documentation](https://www.internationalgenome.org/wiki/Analysis/vcf4.0), QUAL values are phred-scored and indicate the confidence on the assertion made on the ALT allele, whether it is variant or invariant site. That way, QUAL>60 always indicate prob(no-variant) < 10e-6 in v ...
written 6 months ago by
elcortegano • 50
0
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... I want to use `bedtools makewindows` first to create a sliding window over the genome and later to compute GC content with `bedtools nuc`. However, I am having some issues with the makewindows tools, since the intervals seem not to correspond to what is being introduced in the options. For example:
...
written 6 months ago by
elcortegano • 50
1
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2
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156
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... In the end, what worked for me was switching the software. Now I am using [freebayes](https://github.com/ekg/freebayes), which does provide mapping qualities for all variant and invariant sites (e.g. using `--report-monomorphic` option). ...
written 6 months ago by
elcortegano • 50
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