Moderator: Joe

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Joe14k
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JRJHealey
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Recently finished my PhD, so now I pretend to know what I’m talking about on Bioinformatics forums...

Posts by Joe

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Comment: C: Re-mapping contigs or predicted genes?
... Representatives in this context meaning “one E. coli sequence that serves as a reference for all reads that are >`n` amount similar”. You can still use the reads to find SNP variants or something (it might give you more resolution between specific gene sequences), but whether this is needed or n ...
written 12 hours ago by Joe14k
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Comment: C: How to extract promoter sequences from a plant draft genome?
... Looking at that code, it is mainly extracting flanking sites from annotated genes. While this is broadly addressing the goal, this should not be confused with finding *bona fide* promoter sequences, merely the regions where they would actually be found. I say this just in case someone in future com ...
written 2 days ago by Joe14k
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Answer: A: sh: warning: setlocale: LC_ALL: cannot change locale (en_US.utf8)
... You could try the following: Set the locale settings and the `locale-gen` tool: export LC_ALL=en_US.UTF-8 export LANG=en_US.UTF-8 locale-gen en_US.UTF-8 If that fails, try setting the locales to `LC_ALL=C perl`. If this succeeds it will likely be due to having your local machine (the ...
written 2 days ago by Joe14k
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Answer: A: Re-mapping contigs or predicted genes?
... I think there may be some residual confusion, but if we're all on the same page, it does sound like a pangenome analysis problem. If you use a metagenome-aware assembler, to retrieve representatives of every genome in each of your samples, you can then run them through an annotator such as `prokka` ...
written 3 days ago by Joe14k
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Comment: C: Re-mapping contigs or predicted genes?
... I think the assemble and remap approach is fine (this is how you'd do transcriptomics). However, since you're only getting once assembly per set of reads for any given genome, I think what you may need to try is a very strict assembly (few if any mismatches allowed). This is then treated as a refere ...
written 3 days ago by Joe14k
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Comment: C: Re-mapping contigs or predicted genes?
... Are you interested in all variants separately, or are you intending to threshold some similarity scores? i.e. how different can the sequence be in different mutants and strains before its no longer 'the same gene'. Can you also tell us how you assembled all the genomes? I think this is a more sub ...
written 3 days ago by Joe14k
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Comment: C: Re-mapping contigs or predicted genes?
... What you're describing is a `pangenome` study really I think. Are you really interested in actual frequency of the gene, or just in how many organisms in the same have it (and/or have it more than once)? i.e. if there's a billion *E. coli*'s in your sample, do you want to know if there are 2 billi ...
written 3 days ago by Joe14k
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Comment: C: sh: warning: setlocale: LC_ALL: cannot change locale (en_US.utf8)
... Ok yep, you're on a server - are you connecting from a Mac? Have you explored the answers [here?][1] [1]: https://stackoverflow.com/questions/2499794/how-to-fix-a-locale-setting-warning-from-perl/27724459 ...
written 3 days ago by Joe14k
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Comment: C: sh: warning: setlocale: LC_ALL: cannot change locale (en_US.utf8)
... did you connect to a remote server with the `ssh` command? Does the command `echo "$SSH_CLIENT"` return anything other than a blank line? ...
written 3 days ago by Joe14k
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Comment: C: Re-mapping contigs or predicted genes?
... Can you explain a bit further? There may be some terminology confusion here. Firstly, what exactly do you mean by depth/abundance of genes? Is this copy number of the genes, or number of reads corresponding to those sequences etc. "Depth" of gene coverage would only really make sense in the context ...
written 3 days ago by Joe14k

Latest awards to Joe

Commentator 3 days ago, created a comment with at least 3 up-votes. For C: fasta seq header
Appreciated 5 days ago, created a post with more than 5 votes. For C: is fortran still used in bioinformatics?
Commentator 5 days ago, created a comment with at least 3 up-votes. For C: fasta seq header
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar 9 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Commentator 18 days ago, created a comment with at least 3 up-votes. For C: fasta seq header
Scholar 19 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Popular Question 21 days ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Popular Question 23 days ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Commentator 24 days ago, created a comment with at least 3 up-votes. For C: fasta seq header
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar 28 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar 5 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Pundit 6 weeks ago, created a comment with more than 10 votes. For C: is fortran still used in bioinformatics?
Scholar 7 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: How to split a multi fasta file into individual chromosomes
Scholar 8 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar 9 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: fasta seq header
Appreciated 11 weeks ago, created a post with more than 5 votes. For Interesting/useful/beautiful bio sequence viz tools

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