User: Roxane Boyer

gravatar for Roxane Boyer
Roxane Boyer90
Reputation:
90
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Trusted
Location:
France/Marseille/IBDM
Last seen:
1 day, 15 hours ago
Joined:
6 months, 3 weeks ago
Email:
r*************@gmail.com

Posts by Roxane Boyer

<prev • 84 results • page 1 of 9 • next >
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Group a set of plots using MUMmer
... Hello everyone ! This is my first try using MUMmer, I would like to visualize something close to this publication : http://biorxiv.org/content/biorxiv/early/2016/12/02/090969.full.pdf (page 18). I'm trying to align the 6 longest contigs of my assembly to see where it aligns on D.melanogaster genome ...
mummer-plot mummer alignment written 3 days ago by Roxane Boyer90 • updated 3 days ago by skbrimer330
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Comment: C: BWA-MEM using long PacBio reads
... Well, me and some other people are encountering the same problem with blasr. Just look at this issue in github : https://github.com/PacificBiosciences/blasr/issues/324 It indeed seems that it accept only "valid" (whatever it means...) input files. Even if my files come directly from PacBio tools, I' ...
written 3 days ago by Roxane Boyer90
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Comment: C: TPM Transcript per Million : Formula
... When I was confused with the different quantification measures, I used to read documentations of this site : https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/ I hope it could help you a bit with your reflexion ! Woups just saw that you already read ...
written 4 days ago by Roxane Boyer90
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Comment: C: BWA-MEM using long PacBio reads
... Ah, that's indeed what I first thought. Maybe I'll try it later to compare my results with BWA-MEM ! ...
written 4 days ago by Roxane Boyer90
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Comment: C: BWA-MEM using long PacBio reads
... Well, I'm still a student, that's why I'm not always sure about my opinions, and ask a lot of questions. But you guys were right, I don't know how and when, but it seems that the file was corrupted. The last modification date is the 10 January... I didn't even used this file at this moment. I really ...
written 4 days ago by Roxane Boyer90
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Comment: C: BWA-MEM using long PacBio reads
... Hi Charles ! Thanks for your answer. Indeed, I already know Blasr, but I have a lot of trouble with it, the last version is not working anymore, because blasr do not support --bam or --sam option anymore.. That's why I was looking for an alternative ! Bwa mem seems to be the solution ...
written 4 days ago by Roxane Boyer90
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Comment: C: BWA-MEM using long PacBio reads
... Sadly, this is the original file... A collaborator from Munich gave it to me, I downloaded it from a server, and I never modified it. I even used this file to perform an assembly using canu, and Canu worked fine with it... This is very strange. Should I rerun hdf5 tools on it ? Or should I manua ...
written 7 days ago by Roxane Boyer90
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Comment: C: BWA-MEM using long PacBio reads
... Actually, I have absolutely no idea of how to seperate the different lines... Should I use awk ? I like also perl scripts even if it's a bit old school... ...
written 7 days ago by Roxane Boyer90
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Comment: C: BWA-MEM using long PacBio reads
... I actually suspect my raw reads file... Because when I try to type head -1 my_raw_read_file.fastq, everything start is shown on my screen... An example of strange line : ,&**..+-/.+*+".%*"."-&-,+*-..$/,%+&-'#,//,-)%%%+.-++,*.,*+'.--./,-",*/%/+#..$/&/-/.*+-/+-&,.,-+--/+*(,. ...
written 7 days ago by Roxane Boyer90
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Comment: C: BWA-MEM using long PacBio reads
... Sorry for the late reply, it was quite long to re run. Well, sorry as I wasn't totally sure that the ID's were uniq, I opt for the ugly version with the "_". But in fact, it didn't solved my issue, the problem remains the same. head -2 '/media/loutre/SUZUKII/assembly_tries/falcon_aligned_reads. ...
written 7 days ago by Roxane Boyer90

Latest awards to Roxane Boyer

Rising Star 5 months ago, created 50 posts within first three months of joining.
Supporter 5 months ago, voted at least 25 times.

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