User: DNAngel

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DNAngel20
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Posts by DNAngel

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Comment: C: How to set up a reference file for BWA so that highly variable sites between con
... How would I use Blast+ if my organisms don't have references or have the genes sequenced previously?? The reference species exists on ensembl so would that be an option? I do have a lot of reads, each species has over 1 million single-end reads. ...
written 23 days ago by DNAngel20
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How to set up a reference file for BWA so that highly variable sites between conserved regions are detected?
... I use bwa-mem and samtools mpileup to align my species to a reference sequence for a few genes. My problem is that, first, the reference species is somewhat distantly related to the rest of the order I am studying. However, my real problem is that after running bwa-mem and gathering consensus sequen ...
samtools bwa written 23 days ago by DNAngel20
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Comment: C: How do you run codeml for two genes in one file but with 1 species tree?
... Oh I see! Okay that makes sense. I will try that thank you! ...
written 23 days ago by DNAngel20
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Comment: C: How do you run codeml for two genes in one file but with 1 species tree?
... In PAML you typically run one alignment file and one treefile where the species names in the alignment have to exist and match exactly to the names in the treefile. So if I want to double my alignment by adding a gene, I'd have to attach something to the second set of species names like "sp1-2", "sp ...
written 24 days ago by DNAngel20
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How do you run codeml for two genes in one file but with 1 species tree?
... I want to test selection acting on one gene (set as my foreground) compared to a duplicate of the same gene (leaving it as background) but I'm not sure how to set up my files. I have alignments for the two genes, but this means I have to combine them into one alignment file. This means that all my s ...
paml codeml written 24 days ago by DNAngel20 • updated 24 days ago by shelkmike130
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Comment: C: How to distinguish if a gene is a paralogue or an isoform?
... True! When I dug into it deeper and looked up their genomic regions they are indeed located at different points along the chromosome (but still close to each other). Even when reading deeper into a big paper that calls them isoforms, they actually described them as potential paralogs in a figure cap ...
written 4 weeks ago by DNAngel20
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How to distinguish if a gene is a paralogue or an isoform?
... I'm reading up on fish osmoregulation and have come across many papers talking about the expression levels for a very important gene, atpase alpha (NKAa or atp1a1); it has many names. There are different "versions" that are well known such as atpa1a, atpa1b, and atpa1c where each one is expressed di ...
gene paralogue isoform written 4 weeks ago by DNAngel20 • updated 4 weeks ago by kashiff00750
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Comment: C: Can BWA restart a calculation after a break?
... BWA for one species generally isn't that long, it's that my script will automatically run it for 30+ species. The samtools sort however can take a freakin long time and I have no idea how to accommodate that. ...
written 8 weeks ago by DNAngel20
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Comment: C: Can BWA restart a calculation after a break?
... The alignment itself isn't long when I run it for one species - it's the samtools sort that takes a while too. But, my bash script will run the alignment for 30+ species which in total can take 2 days almost! I think I have to just add some pauses in the script which will somehow allow me to continu ...
written 8 weeks ago by DNAngel20
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Can BWA restart a calculation after a break?
... I'm trying to streamline my analyses using bwa and samtools on different servers but I am only allowed to run big processes for 24 hours before it stops processes. The way around this is to have scripts/programs pick up from where it left off (like rsync can do). Is there a way to make bwa and samto ...
samtools bwa written 8 weeks ago by DNAngel20 • updated 8 weeks ago by dariober9.9k

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Scholar 3 months ago, created an answer that has been accepted. For A: How to save trimmomatic terminal summary to an output file?

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