User: Fid_o
Fid_o • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- Last seen:
- 10 hours ago
- Joined:
- 1 year, 7 months ago
- Email:
- s***********@gmail.com
I am a Bioinformatics student, quite new in the field.
0
votes
0
answers
149
views
0
answers
... 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 ...
written 8 months ago by
Fid_o • 20
2
votes
1
answer
565
views
1
answer
... 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? ...
written 8 months ago by
Fid_o • 20
• updated
8 months ago by
Mensur Dlakic • 7.2k
3
votes
1
answer
538
views
1
answer
... 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 ...
0
votes
1
answer
424
views
1
answers
... Thank you sooooo much Mensur Dlakic.
I am learning Bioinformatics and your help is great. ...
written 8 months ago by
Fid_o • 20
3
votes
1
answer
424
views
1
answer
... 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 ...
written 8 months ago by
Fid_o • 20
• updated
8 months ago by
Mensur Dlakic • 7.2k
0
votes
2
answers
193
views
2
answers
... 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_o • 20
2
votes
2
answers
193
views
2
answers
... 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 ...
written 9 months ago by
Fid_o • 20
0
votes
0
answers
137
views
0
answers
... 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 ...
written 9 months ago by
Fid_o • 20
1
vote
1
answer
432
views
1
answer
... 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. ...
written 11 months ago by
Fid_o • 20
• updated
11 months ago by
Mensur Dlakic • 7.2k
0
votes
0
answers
994
views
0
answers
... @jrj.healey use native python functions. The reads/sequences are a million bases. ...
written 19 months ago by
Fid_o • 20
Latest awards to Fid_o
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1972 users visited in the last hour