Moderator: jrj.healey

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jrj.healey7.7k
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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 jrj.healey

<prev • 1,425 results • page 1 of 143 • next >
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Comment: C: So frustrated compiling necessary packages in a linux system
... On most Linux distributions, if you make a `bin` directory under `~`, it will be automatically added to PATH for you ;) ...
written 9 hours ago by jrj.healey7.7k
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Comment: C: So frustrated compiling necessary packages in a linux system
... You shouldn’t need root to use make. ...
written 11 hours ago by jrj.healey7.7k
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Comment: C: So frustrated compiling necessary packages in a linux system
... Alternatively, you may consider installing GVL or BioLinux as your base install image, which comes with a significant amount of software preconfigured. ...
written 12 hours ago by jrj.healey7.7k
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Comment: C: So frustrated compiling necessary packages in a linux system
... Between conda, docker and brew, you can install pretty much everything without root permissions. ...
written 12 hours ago by jrj.healey7.7k
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Comment: C: What are the recommended methods for merging de-novo assemblies?
... If you’re not looking to close the assemblies, and the contigs pass reasonable quality control, you can just leave them. Alternatively, scaffold your contigs so that your small contigs are at least positioned within a final large contiguous assembly. You won’t gain more information, but you’ll make ...
written 23 hours ago by jrj.healey7.7k
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Comment: C: how to find the target sequence for protein modeling?
... Please clarify your question, it is not coherent enough for us to provide much help at this point. ...
written 1 day ago by jrj.healey7.7k
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Comment: C: What are the recommended methods for merging de-novo assemblies?
... This doesn’t seem like a good idea to me because you’ll be introducing variants from different assemblies. You’ll be losing information in some areas and adding erroneous information in others. ...
written 1 day ago by jrj.healey7.7k
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Comment: C: What are the recommended methods for merging de-novo assemblies?
... Try some of these perhaps? https://omictools.com/assembly-reconciliation-category I can’t personally speak to any of them as I’ve never tried what you’re attempting. ...
written 1 day ago by jrj.healey7.7k
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Comment: C: What are the recommended methods for merging de-novo assemblies?
... Yep, Damiens answer was where I was headed. Just concatenate all you R1s and all your R2s and assemble that. Depending on the quality, you may not want to use all of them. If you have some which are lower quality, there’s no point ‘tainting’ your other reads with them. 88 lots of fastqs may also l ...
written 1 day ago by jrj.healey7.7k
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Comment: C: Python Script to Calculate Total Number of genes
... Then use a proper gene finding tools such as GeneMark or Glimmer. Writing a python script to identify which ORFs are legitimate genes is not going to be simple. Alternatively, use an annotation pipeline like PGAP/PROKKA, and then use biopython to count the number of `gene` or `CDS` tags that are d ...
written 1 day ago by jrj.healey7.7k

Latest awards to jrj.healey

Scholar 1 day ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 3 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 4 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 5 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 5 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
Teacher 8 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 8 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 10 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 10 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 12 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 12 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
Appreciated 17 days ago, created a post with more than 5 votes. For A: Replace Sequence IDs in many text files (newick format) - Change script
Teacher 17 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
Teacher 19 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
Popular Question 21 days ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Teacher 22 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
Commentator 23 days ago, created a comment with at least 3 up-votes. For C: fasta seq header
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Replace Sequence IDs in many text files (newick format) - Change script
Scholar 5 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
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
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
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
Teacher 6 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 6 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence

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