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User: Roxane Boyer

gravatar for Roxane Boyer
Roxane Boyer • 210
Reputation:
210
Status:
Trusted
Location:
France/Marseille/IBDM
Last seen:
3 weeks, 5 days ago
Joined:
1 year ago
Email:
r*************@gmail.com

Posts by Roxane Boyer

<prev • 126 results • page 1 of 13 • next >
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Calculate numbers of indels <=2 nt within sam
... Hello everyone, I am really bad at manipulating sam files... I was looking for a simple way to count, within a sam, the number of indels <=2 nucleotides. I also want it to be position specific, which means for me that, for a single position, if I have a read coverage of 100 and in each read ther ...
script written 6 weeks ago by Roxane Boyer • 210 • updated 6 weeks ago by Pierre Lindenbaum ♦ 96k
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Comment: C: [PacBio assembly] Remaining indels after polishing
... Yeah of course, I know I should trust them. I want to correct indels regarding RNAseq mapping indications. If RNAseq mapping indicate that there is an indel, then I want to correct it. But I want a way to estimate how many indels like this I have in my assembly, and how to correct them without doing ...
written 7 weeks ago by Roxane Boyer • 210
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Comment: C: [PacBio assembly] Remaining indels after polishing
... In fact, I didnt used Pilon to correct the data, I used quiver with pacBio reads, so our approaches are different. The pacbio sequencing coverage is supposed not to be impacted by GC%. I don't really know what is going on there ...
written 7 weeks ago by Roxane Boyer • 210
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Comment: C: [PacBio assembly] Remaining indels after polishing
... Indels are like a single nucleotide inserted, or missing, it is not assembly wide, just in a particular regions that I was able to find this. The numbers, I can't say exactly, because I am not sure that there is not other case else where in my assembly. In the concerned region, it was like maximum 1 ...
written 7 weeks ago by Roxane Boyer • 210
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[PacBio assembly] Remaining indels after polishing
... Hello everyone ! I am currently de novo assembling a drosophila genome, with a high level of polymorphism, using long PacBio reads. As my sequencing coverage is enough (220x), I chose to use the "PacBio" only method, which consist in "polishing" the final assembly by aligning raw reads against it a ...
assembly polishing pacbio quiver written 7 weeks ago by Roxane Boyer • 210 • updated 7 weeks ago by Gedankenstuecke • 0
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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 9 weeks ago by Roxane Boyer • 210
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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 9 weeks ago by Roxane Boyer • 210
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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 9 weeks ago by Roxane Boyer • 210
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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 9 weeks ago by Roxane Boyer • 210
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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 9 weeks ago by Roxane Boyer • 210

Latest awards to Roxane Boyer

Popular Question 3 months ago, created a question with more than 1,000 views. For Training Augustus for Maker
Appreciated 4 months ago, created a post with more than 5 votes. For A: What can I do after my Pacbio genome assembly ?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What can I do after my Pacbio genome assembly ?
Centurion 4 months ago, created 100 posts.
Scholar 6 months ago, created an answer that has been accepted. For A: Trouble with Pilon installation
Rising Star 11 months ago, created 50 posts within first three months of joining.
Supporter 11 months ago, voted at least 25 times.
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