User: Fid_o

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Fid_o20
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10 hours ago
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1 year, 7 months ago
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I am a Bioinformatics student, quite new in the field.

Posts by Fid_o

<prev • 24 results • page 2 of 3 • next >
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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 8 months ago by Fid_o20
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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 8 months ago by Fid_o20 • updated 8 months ago by Mensur Dlakic7.2k
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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 8 months ago by Fid_o20 • updated 6 weeks ago by herber420
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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 8 months ago by Fid_o20
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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 8 months ago by Fid_o20 • updated 8 months ago by Mensur Dlakic7.2k
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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 9 months ago by Fid_o20
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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 9 months ago by Fid_o20
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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 9 months ago by Fid_o20
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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 11 months ago by Fid_o20 • updated 11 months ago by Mensur Dlakic7.2k
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Comment: C: Python Script to map reads to reference sequence
... @jrj.healey use native python functions. The reads/sequences are a million bases. ...
written 19 months ago by Fid_o20

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