User: rosies

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rosies0
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Posts by rosies

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Comment: C: How to determine sample clusters from phylogeny
... Fantastic. Thank you Joseph. I tried it on my data (just the gui) but it doesn't look like it likes my dataset (112 samples at ~3MB each). I'll try via command line on the HPC to see if this works. ...
written 3.1 years ago by rosies0
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Comment: C: How to determine sample clusters from phylogeny
... Hi Ron, I'm a bit naive in the space of clustering algorithms, but, yes, hierarchical clustering looks good. I'm hoping the clustering algorithm can divide clades into clusters (and provide a statistic for where it calculates where a clade/cluster starts/ends). Do you have any recommendations for so ...
written 3.1 years ago by rosies0
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How to determine sample clusters from phylogeny
... Hi, I have constructed a phylogenetic tree (Roary, FastTree) of outbreak bacterial isolates (staph) and am wondering how I can determine which isolates form a cluster. Also, do you have any advice on how to be consistent with cluster definitions when more isolates are added to the analysis. Thank y ...
phylogeny cluster detection written 3.1 years ago by rosies0 • updated 3.1 years ago by Joseph Hughes2.8k
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reduced quality of lane 4 compared to other lanes (paired-end Illumina)
... Hi there, I have paired end Illumina (NextSeq) data (Staph aureus, avg sequence length 150bp). After running FastQC, I found reads from Lane 4 R2 to have reduced quality compared to that in Lane 1-3, R1 and R2. With most Lane 4, R2 from my samples (100+ samples) I would need to trim 30 bps whereas ...
sequencing written 3.1 years ago by rosies0
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How to generate Artemis ACT comparison file of multiple sequence alignment
... Hi there, I was wondering how you would generate a comparison file for a single multiple sequence alignment file to be used with Artemis ACT. Thanks, Rosie ...
act artemis comparison file msa written 4.6 years ago by rosies0 • updated 20 months ago by Joe15k
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Multiple sequence alignment editor that can load feature embl files
... Hi there, I have a multiple sequence alignment of 48 sequences each of 3Mbp in length (large), generated using Mafft. I have generated an embl and gff file of recombination sites from Gubbins. I would like to remove these sites from each of the 48 strains. I was wondering whether there was a progra ...
editor alignment embl written 4.6 years ago by rosies0
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Comment: C: Multiple sequence alignment of sequenecs of different length
... Thank you arnstrm, this worked a treat! ...
written 4.6 years ago by rosies0
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Multiple sequence alignment of sequenecs of different length
... Hi there, I have the consensus sequence for 48 strains that I have mapped and aligned to a reference using CLC. They are each of approx 3Mbp (about 100bp difference in lengths between the sequences). I am trying to perform a time divergence analysis, but before that I need to format my sequences so ...
multiple sequence alignment written 4.6 years ago by rosies0 • updated 4.6 years ago by arnstrm1.7k

Latest awards to rosies

Popular Question 2.8 years ago, created a question with more than 1,000 views. For How to generate Artemis ACT comparison file of multiple sequence alignment
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Multiple sequence alignment of sequenecs of different length

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