User: memory_donk

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memory_donk250
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Australia
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Posts by memory_donk

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Method for generating a reference-based genome assembly in fasta with no referen
... I think what I wound up doing was running samtools mpileup but excluding the -f flag and reference genome. At least as far as I could tell, I didn't find bases that came from the reference instead of the data. That could have also been because I had ~50X coverage, had a very high mapping percentage ...
written 14 months ago by memory_donk250
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Comment: C: Problem improving mammal contig assemblies
... So I've tried downsampling like people suggested in the comments without any success. The difference in contig size was basically trivial. I've tried 200X, 150X, 70X, 50X, 40X and 30X with very little difference in the result (a few hundred bp or so) and the largest contig has hardly changed in size ...
written 2.4 years ago by memory_donk250
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Comment: C: Problem improving mammal contig assemblies
... If anyone around has other suggestions I'd really appreciate it. I've tried downsampling and error correcting but neither made more than a trivial difference in contig N50. Everything I can tell about this dataset says its excellent quality of but I can't get even half-decent contigs. ...
written 2.4 years ago by memory_donk250
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Answer: A: Platanus file format error
... Ok so I just had the exact same problem and after losing about half of my hair I figured it out. BFC outputs some letters as lowercase and Platanus doesn't seem to like that. I used a sed one-liner to convert all bases to uppercase and it started running. Obviously only use this on fasta or you coul ...
written 2.4 years ago by memory_donk250
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Is baseml (PAML) suitable for ancestral reconstruction of non-coding sequences?
... Hi Biostars, I'm not super familiar with the underlying data used to general substitution models or how programs like PAML utilise them for ancestral reconstructions. I'm hoping though, to do ancestral reconstructions of several non-coding (putative enhancer) sequences and wasn't sure whether PAML' ...
ancestral reconstruction evolution written 2.4 years ago by memory_donk250
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Comment: C: Gene Ontology term enrichment tools that count duplicate/redundant genes
... That's a really interesting idea Carlo, I hadn't thought to rank GOrilla inputs like that. Edit: Thinking about this though, even ranking still doesn't quite capture the frequency of GO terms associated with nearby genes. In principle, each GO term ought to be counted once for every occurrence of a ...
written 2.4 years ago by memory_donk250
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Gene Ontology term enrichment tools that count duplicate/redundant genes
... Hi Biostars, I've got a list of putative enhancer elements that I've predicted based on conservation, epigenetic marks etc etc and a subset of these which are predicted to be rapidly evolving. I would like to do a Gene Ontology analysis on nearby genes. However, most GO tools take your input list o ...
geneontology go genomics ontology written 2.4 years ago by memory_donk250 • updated 2.4 years ago by Carlo Yague4.6k
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Comment: C: Problem improving mammal contig assemblies
... Hi Asaf, I think you and Sej are on the right track. I looked back at my previous assemblies and can see the total assbly size is quite a bit larger than it ought to be (suggesting many extra contigs, possibly due to errors). I also ran one of my smaller sets of reads (~50X) and it improved the asse ...
written 2.5 years ago by memory_donk250
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Comment: C: Problem improving mammal contig assemblies
... I have long insert libraries. My question was about contig assembly so they are irrelevant my main issue was also with SOAPdenovo2 as I said. Ill try SGA and see if that provides any new info. Thanks ...
written 2.5 years ago by memory_donk250
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Comment: C: Problem improving mammal contig assemblies
... Thank you Sej, I'll give that a try. ...
written 2.5 years ago by memory_donk250

Latest awards to memory_donk

Popular Question 2.2 years ago, created a question with more than 1,000 views. For Tree input for PAML ancestral state reconstruction
Good Answer 3.0 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 3.4 years ago, created an answer that has been accepted. For A: How To Get Ensembl Id (Gene, Transcript, Protein) Information?
Teacher 3.4 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 3.4 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 3.4 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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