User: memory_donk

gravatar for memory_donk
memory_donk250
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Australia
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1 year, 3 months ago
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3 years, 10 months ago
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Posts by memory_donk

<prev • 30 results • page 2 of 3 • next >
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Comment: C: Problem improving mammal contig assemblies
... Thanks for your reply. I'm just not certain how subsampling is a strategy for dividing the dataset and combining resulting assemblies. Writing a script to take random reads out of a file is easy, making high-quality assemblies from multiple smaller assemblies is a somewhat different problem though. ...
written 2.6 years ago by memory_donk250
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Problem improving mammal contig assemblies
... Hi Biostars, I was hoping someone may be able to give some guidance about troubleshooting a mammalian genome assembly. My species has a similar genome size to humans and I have ~150X coverage of 2x150bp Illumina reads for building contigs. I've previously had modest luck assembling contigs for a c ...
genome assembly written 2.6 years ago by memory_donk250 • updated 2.6 years ago by h.mon27k
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Scripting method to parse fastq diploid consensus sequence bins based on quality
... Hi Biostars, I need to write a script that will accept scaffolds from a diploid consensus sequence in fastq format like one generated by this command [1], break the sequence into non-overlapping bins of 100bp, and give a true or false output based on whether they were above some quality threshold. ...
fastq bioperl biopython parsing written 3.4 years ago by memory_donk250
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Estimating PSMC -p parameter and missing heterozygotes
... Hi Biostars, My advisor wants me to run PSMC on a data set we've generated (because I'm the only one in the lab who can sort of script and use Linux). I've read the manual on the github page, the original paper (and googled for answers), but I fundamentally don't understand the -p parameter or how ...
psmc written 3.4 years ago by memory_donk250 • updated 3.4 years ago by Zev.Kronenberg11k
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Answer: A: How to calculate p-value from codeml likelihood ratio test results for Benjamini
... I apologise for positing this and then answering my own question, I hope I haven't broken a site rule (if so please feel free to delete this post, though I'll leave it up for now in case anyone else runs into a similar problem). This is a classic case of RTFM, because I haven't read the whole (huge ...
written 3.4 years ago by memory_donk250
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How to calculate p-value from codeml likelihood ratio test results for Benjamini-Hochberg correction
... Hi Biostars I'm doing positive selection analysis on a relatively large set of orthologous genes using PAML's implementation of the branch-site model. I've got the results of my likelihood ratio test (LRT) for each gene, and according to this (1) and other papers, the branch-site model follows a 1: ...
statistics paml codeml lrt written 3.4 years ago by memory_donk250
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Answer: A: How To Get Ensembl Id (Gene, Transcript, Protein) Information?
... Ensembl BioMart is probably your best bet. You may need to use/write a quick script or awk command to extract your chromosome number and position but you can enter a list of chromosomal positions in the filter menu under regions->multiple chromosomal positions. You can then choose which attribu ...
written 3.5 years ago by memory_donk250
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Comment: C: perl scriot for fasta
... Here is a link to the beginners HOWTO on the Bioperl wiki. It gives you an introduction to the sequence and seqIO objects. If you learn these you can do pretty much anything in terms of basic fasta parsing/manipulation http://www.bioperl.org/wiki/HOWTO:Beginners ...
written 3.5 years ago by memory_donk250
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Answer: A: Why does base quality of reads generally decreases at the end of the read?
... The really specific answer depends on what platform you're using but I'll go out on a (short) limb and guess its Illumina. If so, the drop-off is a phasing error. With Illumina, DNA fragments are first bound to a flow cell. A well-prepared flow cell has even spacing between all DNA fragments. Befor ...
written 3.5 years ago by memory_donk250
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Answer: A: How to fix mates in PE Illumina data after alignment and discard reads with no m
... I'm sure there are bigger-name pieces of software that will do it, but these scripts by the MacDonald lab are pretty quick and easy and have good instructions. You need Picard installed to use them but they're written in Perl http://www.mcdonaldlab.biology.gatech.edu/bioinformatics.htm edit: no af ...
written 3.5 years ago by memory_donk250

Latest awards to memory_donk

Popular Question 2.3 years ago, created a question with more than 1,000 views. For Tree input for PAML ancestral state reconstruction
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: Why does base quality of reads generally decreases at the end of the read?
Scholar 3.5 years ago, created an answer that has been accepted. For A: How To Get Ensembl Id (Gene, Transcript, Protein) Information?
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Why does base quality of reads generally decreases at the end of the read?
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Why does base quality of reads generally decreases at the end of the read?
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Why does base quality of reads generally decreases at the end of the read?

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