User: Fido

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Fido20
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1 week ago
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11 months, 3 weeks ago
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I am a Bioinformatics student, quite new in the field.

Posts by Fido

<prev • 15 results • page 1 of 2 • next >
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Generating Neighbour Joining Tree from Sequences
... I would like to generate a Neighbour Joining (NJ) tree from a FASTA alignment I have (from bacterial sequences). What better software is available for this? ...
genome sequence snp written 15 days ago by Fido20 • updated 15 days ago by lagartija80
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Lineage Separation of Bacterial Sequences
... Greetings, I have a group of sequences from bacterial genome which I want to separate into lineage-sublineage. I have reference genome for the parent lineage and a reference genome for the sublineage. These are separated by differences in SNPs. What good software or code would I use to pull out th ...
gene alignment sequence snp written 24 days ago by Fido20
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CONVERT .aln file to .phy for RAxML input
... I ran roary on sequences and I have an aligned file with the extension .aln. I would like to run this aligned file on RAxML which needs a .phy file. How do I convert .aln file to sequential .phy? ...
alignment written 28 days ago by Fido20 • updated 28 days ago by Mensur Dlakic4.3k
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Visualising Roary Results
... I run roary ( roary -e --mafft -p 32 *.gff) to produce core genome alignment on hundreds of Salmonella sequences and have results. I have the following files in the results: 1. gene_presence_absence.csv 2. gene_presence_absence.Rtab 3. pan_genome_reference.fa 4. accessory_binary_genes.fa.newick 5 ...
genome sequence alignment roary snp written 28 days ago by Fido20 • updated 28 days ago by zx87549.1k
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Comment: C: Genome Annotation Output Files Naming
... Thank you sooooo much Mensur Dlakic. I am learning Bioinformatics and your help is great. ...
written 4 weeks ago by Fido20
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Genome Annotation Output Files Naming
... I ran this annotation command: for k in *.fasta; do prokka $k --outdir "$k".prokka.output; echo $k; done on hundreds of assembled sequences. Each sequence annotation output produced a folder named "sequence_name.prokka.output" but the actual files in the folders were named according to the date e ...
genome annotation written 4 weeks ago by Fido20 • updated 4 weeks ago by Mensur Dlakic4.3k
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Comment: C: Filtering Whole Genome Sequence Data
... Greetings @ATpoint! Thanks for that reply. I want to do core and accessory gene analysis using roary. I will later be doing phylogenetics. I want to remove all sequences that are too small or too large as, from what I was told, a too small size would mean only a shorter part of the genome was sequ ...
written 4 weeks ago by Fido20
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Filtering Whole Genome Sequence Data
... I have whole genome sequence data (.FASTA files) for Salmonella bacteria. On average the sequence files have a size of 4.7MB but there are some that are too big, like 7Mb and others that are too small, like 500Kb. There is likelihood that the too large files contain unnecessary sequence data and the ...
genome sequence written 4 weeks ago by Fido20
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Salmonella Typhimurium Strain Lineage
... I have 900 assembled Salmonella Typhimurium ST313 sequences (.FASTA files, average sequence size 4.7MB). Basic information says there are two lineages of salmonella strains - one an old lineage and another a newer one. The newer one has 22 SNP differences from the old one. I need to separate which ...
lineage salmonella snp linux written 4 weeks ago by Fido20
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Prokka Python Script for Gene Annotation
... I have over 900 assembled genomes which I want to annotate using prokka. Previously I have annotated few sequences by running each one by one, but with 900 I need a python script to automate the process. Can anyone share a script that can be adopted to do my annotation, please. Regards. ...
python annotation script prokka linux written 3 months ago by Fido20 • updated 3 months ago by Mensur Dlakic4.3k

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