User: Roxane Boyer

gravatar for Roxane Boyer
Roxane Boyer220
Reputation:
220
Status:
Trusted
Location:
France/Marseille/IBDM
Last seen:
4 days, 9 hours ago
Joined:
11 months ago
Email:
r*************@gmail.com

Posts by Roxane Boyer

<prev • 121 results • page 1 of 13 • next >
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Comment: C: [BioPython] Parse blast tabular output
... That is awesome ! I was doing the exact same steps you did before I realised that Biopython may already implemented it... But yours is way better, I think I may use it a lot ! thanks again ...
written 6 days ago by Roxane Boyer220
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Comment: C: [BioPython] Parse blast tabular output
... Really ? Ow damn, I was stucked with this question for so long... Thanks a lot then I'm going to try ! it sounds dumb now ...
written 6 days ago by Roxane Boyer220
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Comment: C: [BioPython] Parse blast tabular output
... About doing the parser myself without biopython, I already thought about that, But I was stucked at the part where I had to read powered numbers with python... Like when you have something like this : 5e-43, how do you store this in python ? It's been a while since I didn't worked in python... ...
written 6 days ago by Roxane Boyer220
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Comment: C: [BioPython] Parse blast tabular output
... Ah right I remember, parse from searchIO support only xml so that's why I'm not happy with it ...
written 6 days ago by Roxane Boyer220
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Comment: C: [BioPython] Parse blast tabular output
... SearchIO is a nice suggestion, though my blast result will contain a lot of raws, and the function read can work only with blast output with exactly one result. But searchIO has also a parse function, which handle multi result blast file, but when I tried it didn't worked. I'm trying again see if y ...
written 6 days ago by Roxane Boyer220
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[BioPython] Parse blast tabular output
... Hi everyone, I am trying to parse a blast result produced using outfmt 6 option. I have made several tries, with iterators, without iterators... But each time it fails to parse my file. Here some code that I try : parser = argparse.ArgumentParser() parser.add_argument("blast_file", help="Th ...
python biopython blast written 6 days ago by Roxane Boyer220 • updated 6 days ago by a.zielezinski6.9k
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Comment: C: Removing contaminations from PacBio reads
... Hi Ric, did you managed to solve your issue using Genomax answer ? I'm still stuck with this question, because I don't now yet all organism that contaminated my assembly. Any others suggestions ? I was thinking about blasting maybe a sequence highly specific to bacteria, which is shared among bacter ...
written 6 days ago by Roxane Boyer220
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Comment: C: What can I do after my Pacbio genome assembly ?
... Hi Picasa ! Sadly, I never managed to get arrow to work on my computer (installation issue), same thing with the others algorithm... I will try to test it again, I also really want to know how different the two algorithm work, and especially want to know if one of them is parallelizable (as quiver ...
written 26 days ago by Roxane Boyer220
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Descrease annotation running time by spliting contigs into separated files (maker)
... Hi everyone ! I am using the tool maker to annotate my genome. The problem is that this tool is not using several cores to do the task. So I was wondering, what about splitting my genome assembly contigs into several five (let's said 32, my number of CPU). For example, if I have 64 contigs, the 2 ...
genome annotation maker written 6 weeks ago by Roxane Boyer220
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Polishing PacBio assembly : The ideal coverage for higly polymorphic species
... Hello everyone ! I need a few advices regarding the final step of my *D. suzukii* assembly, using long PacBio reads : the polishing step. First, let me explain how I obtained the file I am working on. I have made two different assembly using different algorithms : Falcon and Canu. I have assessed ...
polishing busco pacbio genome assembly written 6 weeks ago by Roxane Boyer220

Latest awards to Roxane Boyer

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Training Augustus for Maker
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: What can I do after my Pacbio genome assembly ?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: What can I do after my Pacbio genome assembly ?
Centurion 11 weeks ago, created 100 posts.
Scholar 4 months ago, created an answer that has been accepted. For A: Trouble with Pilon installation
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