User: Picasa

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Picasa270
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Posts by Picasa

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Comment: C: Best de novo genome assemblies using only Illumina data ??
... Maybe I was not clear with my question. I am not asking which assembler is the best, but I am looking just for papers with different project that have done a de novo genome assembly and had good results. (like the panda genome) http://www.nature.com/nature/journal/v463/n7279/full/nature08696.htm ...
written 2 days ago by Picasa270
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Best de novo genome assemblies using only Illumina data ??
... Hi, I am looking for papers of the best de novo assemblies ever done with (and only) Illumina data for differents kind of organisms (bacteria, insect, mammals, plants etc.) By best I mean accurate, not fragmented (high N50), no contaminations, good completeness scores etc. Do you know any ? Than ...
de novo assembly illumina written 2 days ago by Picasa270
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Comment: C: What can I do after my Pacbio genome assembly ?
... I have the sequencing coverage information; but why is it important ? ...
written 21 days ago by Picasa270
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Comment: C: What can I do after my Pacbio genome assembly ?
... Hi Roxane and many thanks for your help ! However I don't have .bas/bax.h5 files but only fastq (my raw reads are fastq files) so can I still use pbalign with your command ? I mean, does it recognize fastq ? ...
written 22 days ago by Picasa270
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What can I do after my Pacbio genome assembly ?
... Hi I have just assembled my genome with CANU. I am a beginner with Pacbio data and I am wondering now if there is something I can do more ? 1) I heard about Quiver for polishing the assembly: For this I think I need a sam file where my reads have been mapped to my genome. Can I use the mapper blas ...
pacbio written 22 days ago by Picasa270 • updated 22 days ago by Roxane Boyer180
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Comment: C: Most represented reads in SAM file
... Sorry I forgot to mention that I use BWA with the option -M And yes mapping the same location (because the same reads). ...
written 22 days ago by Picasa270
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Comment: C: Most represented reads in SAM file
... Yes same sequences (at 100%). ...
written 23 days ago by Picasa270
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Most represented reads in SAM file
... Hi, I am looking for your help. I have a SAM file (with paired reads that I have mapped against a reference) and I would like to extract the paired read which is the most represented (or most abundant). I want to select the paired read the most covered for a particular reference. Is there a tool ...
reads sam representated written 23 days ago by Picasa270
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Comment: C: Mismatch setting for bwa mem ?
... This is the mismatch penalty for the score but it does not say how many mismatchs are allowed ...
written 9 weeks ago by Picasa270
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Mismatch setting for bwa mem ?
... Hi, Can we set the mismatch number for bwa mem ? And by the way what is the default number ? Thanks ...
bwa mem mismatch written 9 weeks ago by Picasa270

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For Best strategy for de novo assembly with illumina reads ?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Best strategy for de novo assembly with illumina reads ?
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Scholar 8 months ago, created an answer that has been accepted. For A: 16S Paired-End Illumina MiSeq Data in Qiime
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