User: anamaria

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anamaria30
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anamariaelek
Last seen:
5 days, 11 hours ago
Joined:
11 months ago
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Posts by anamaria

<prev • 8 results • page 1 of 1 • next >
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Comment: C: add UMI sequences to fastq read name
... I'm also curious, what bases mask did you use for the demultiplexing to get these three fastqs? ...
written 6 weeks ago by anamaria30
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Answer: A: Can we concatenate two fastq files from same sample but different runs
... If I am not wrong, `--no-lane-splitting` is only available for `bcl2fastq2`, not for the `bcl2fastq`. ...
written 3 months ago by anamaria30
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Comment: C: Size of typical genomic data
... I would like to have a look at this report, if you could send it please? Thank you ...
written 6 months ago by anamaria30
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Tool: Analysis of codon usage in R/Bioconductor using coRdon
... We have developed coRdon, an R package for the analysis of codon usage in various unannotated or KEGG/COG annotated DNA sequences. Features: coRdon can be used to **easily calculate** several **different measures** of codon usage (CU) bias and CU-based predictors of gene expressivity, including EN ...
R tool codon usage written 10 months ago by anamaria30
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Comment: C: Codon Adaptation Index
... Cool, will do, thank you ...
written 10 months ago by anamaria30
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Answer: A: Generating Codon Usage
... Leaving this here for the future reference... Following up on the concatenation approach, you could make use of the Bioconductor packages in R to do this: concatenate the sequences using Biostrings, and then analyse codon usage with coRdon. https://bioconductor.org/packages/release/bioc/html/Biostr ...
written 10 months ago by anamaria30
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Answer: A: Codon Adaptation Index
... For those interested in calculating codon usage statistic, including CAI, there's our R/Bioconductor package that lets you do this, and it comes with some nice visualisations, too https://bioconductor.org/packages/release/bioc/html/coRdon.html ...
written 10 months ago by anamaria30
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Comment: C: annotation of SV (structural variants)
... Hi Daniel, I have tried processing delly v0.7.9 output vcf file with `breakpointRanges()` and all of the BNDs were removed as unpaired, so I was wondering if there was a way around this issue, using your package? ...
written 11 months ago by anamaria30

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