7
votes
How can I add a ";" at the end of each fasta header line in a file?
One way, using sed and a regex address to select only the header lines and apply a substitution to append a semicolon to the end of each line:
...
- 3,059
6
votes
How can I add a ";" at the end of each fasta header line in a file?
... using the legendary Perl pie
perl -p -i -e 's/^(>.*)/$1;/' mybacteria.fa
Input
...
M__♦
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4
votes
Extract reads from bam files by their @RG
Typically I use samtools for operations like this. Specifically I use samtools view with either -r or ...
- 2,574
4
votes
Gene function annotation - bacterial genome
The PATRICBrc.org is a free resource you can annotate your genome and compare it with publicly available genomes.
Refer this tutorial for more detail.
Once you have annotated your genome in PATRIC, ...
- 143
4
votes
How to quantify similarity of genomes and find differences in set of S aureus genomes?
... stuff of original post deleted.
On second thoughts what you might be doing is a template assembly of your genomes. It is a possible interpretation of the 1.2. fasta sequences above (i.e. 1 is ...
M__♦
- 11.9k
4
votes
Accepted
Questions about microbial 16s rRNA phylogenetic, ANI Taxonomy, and GGDC
I do understand that you are working with is an isolate and thus what occurs in metagenomics you feel is over doing it, particularly if 16S is e.g. >99% similarity via Blast.
Before reading ...
M__♦
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4
votes
How to display novel genome assemblies or uncommon genome assemblies using the UCSC Genome Browser?
I found two methods:
You want to visit this page for instructions for novel assemblies: http://genomewiki.ucsc.edu/index.php/Assembly_Hubs .
However, before doing that I highly recommend that you ...
- 596
3
votes
Accepted
Populations genetics and dynamics of bacteria on a Graph
I assume you are simulating a null distribution. Are you investigation recombination??
My main advice is to use population genetic terminology rather than geomometry to describe your simulation (e.g. ...
M__♦
- 11.9k
3
votes
How can I add a ";" at the end of each fasta header line in a file?
I recommend to use Biopython as a clearer way.
...
- 435
3
votes
How can I add a ";" at the end of each fasta header line in a file?
seqkit replace -p "$" -r ";" my.fasta > my.renamed.fasta
Where -p is the pattern to match the end of ...
- 143
3
votes
Accepted
How to fragment genomes into non-overlapping sequences of differing sizes?
You could use numpy.random.randint to sample integers from a uniform distribution, from 1000 to 15000 nt, extracting subsequences of that length from a linearized ...
- 3,125
3
votes
Accepted
Should I expect / use a prokaryote-specific substitution model when building a phylogenetic tree?
IQTree is a fashionable method for speeding up bootstrapping and used on ultra large datasets. What IQTree might be doing is rigidly fixing a model and parameterisation is not estimate via the ML. ...
M__♦
- 11.9k
3
votes
Accepted
Barrnap Bacterial rRNA Predictor script permission denied error when running Prokka
My suggestion is to run prokka from within conda by simply downloading miniconda then
...
M__♦
- 11.9k
2
votes
how do I predict bacterial small non-coding RNA for a specific mRNA?
Answer from @llrs, converted from comment:
You could try to download RNAseq data from this bacteria and see if some of the RNA align to your sequence. You could try to blast your gene and look for the ...
2
votes
Accepted
CRISPR Sequence Finder and Database Download
CRT (CRISPR Recognition Tool) http://www.room220.com/crt/
Crisprs Finder Online Tool https://crispr.i2bc.paris-saclay.fr/Server/
Piler-CR http://www.drive5.com/pilercr/
(Omic Tools List) https://...
- 173
2
votes
Extract reads from bam files by their @RG
This sounds more like a job for samtools split if you want to split out all the read groups into separate bams in one go.
http://www.htslib.org/doc/samtools-split....
2
votes
Looking for a tool to find 16S rRNA in hundreds of genomes
You can use Barrnap
barrnap -k bac --threads "$(nproc)" \
-o output_rrna.fna < input_file.fna \
> output_rrna.gff 2> /dev/null
Put the ...
- 769
2
votes
Is there a "definitive" database for Mobile Genetic Elements?
Would advise doing Denovo identification method structure-based. Then use these public databases ( RepBase, Dfam ) to look for high similarity or homology exploration, this possibility if your ...
- 374
2
votes
Accepted
How can I improve or otherwise investigate an unreliable genome tree?
The difficulty in answering the question is:
The absence of "Y" in the "Gene of interest" tree
The sampling bias in the number of taxa mostly between the "genome tree" ...
M__♦
- 11.9k
2
votes
Accepted
Bacterial genomes and snpeff warnings 'WARNING_TRANSCRIPT_NO_START_CODON'
Bacteria have a different translation table from eukaryote nuclear DNA; it may be that SnpEff is expecting human genes in the genome. Have you followed the build steps outlined in the documentation?
...
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2
votes
What would be the best method to obtain every prokaryotic psychrophile genome?
The database to use is BactoTraits. This will help either in the entirety or at least provide a solid starting point. Its here
BactoTraits – A functional trait database to evaluate how natural and man-...
M__♦
- 11.9k
2
votes
Accepted
What would be the best method to obtain every prokaryotic psychrophile genome?
I ended up copying the GenBank (primary) column from the REBASE search results into an excel sheet. From there, I created a file with one accession per line called ...
- 163
2
votes
Accepted
Genetic relationships between Cyanobacteria: terrestrial vs aquatic
Ah! Finally, a question I can answer.
There has been some pretty good work about this recently. In particular, I would reccomend this paper by Chen et al. , which groups cyanobacteria into terrestrial ...
- 881
1
vote
How can I improve or otherwise investigate an unreliable genome tree?
It seems like you've got the right approach, in trying out a few different genes and looking for consistency. As you say, different genes can have different selective pressures, which influences how ...
- 13.8k
1
vote
How to display novel genome assemblies or uncommon genome assemblies using the UCSC Genome Browser?
I am not sure if this qualifies as an official answer. I have contacted UCSC bioinformatics team. They were were very kind and told me that they would add any track that was requested by users. After ...
- 596
1
vote
Bruker MALDI-TOF bacteria species identification scoring algorithm
For identification scoring, the software correlates signal
intensities of matched signals of mass spectra. The three scores
obtained from such a procedure are multiplied and normalized to a
value of 1,...
- 151
1
vote
Accepted
How can I get or create a reference genome for Bacteria?
How can I get a reference sequence for other strains of E. coli?
You can use any sequence you want as reference for a variation analysis. It just depends on the question you want to answer.
So to ...
- 629
1
vote
How to fragment genomes into non-overlapping sequences of differing sizes?
I've previously written my own script to fragment DNA sequences (input as either fastq or fasta files) into identical-length fragments, with a given overlap. I used this because there was a particular ...
- 13.8k
1
vote
Bacterial DNA at the tail of transcriptome reads. What does that mean?
What exactly is the sequence? Are you sure it's not an artifact of the library prep?
5 seconds of googling turns up this:
https://support.illumina.com/content/dam/illumina-support/documents/...
- 1,882
1
vote
Bacterial DNA at the tail of transcriptome reads. What does that mean?
From time to time these situations are encountered, notably when PCR is being deployed in rare DNA samples.
In this instance the wiki states,
Ralstonia solanacearum is an aerobic non-spore-forming,
...
M__♦
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Only top scored, non community-wiki answers of a minimum length are eligible