User: pmarijon

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pmarijon100
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pierre_marijon
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Posts by pmarijon

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Want to use fastq-dump to download pacbio data? Read this before
... "You'd be surprised by the incredible story of this simple student when he uses the wrong tools to get reads" ...
written 8 days ago by pmarijon100
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Comment: C: You want use fastq-dump to download pacbio dataset before read that
... Hi WouterDeCoster, Thanks I change the title I hope it's more clear now ? (now this is a question :) ) Pierre ...
written 10 days ago by pmarijon100
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Blog: Want to use fastq-dump to download pacbio data? Read this before
... TL;DR I think not, prefer use dextractor Recently I downloaded the NCTC11131 data set stored at EBI via the fastq-dump tool. I would like to assemble it with miniasm and minimap in order to reproduce results from te HINGE paper. The obtained assembly was very fragmented with 34 contigs while HINGE ...
blog longreads written 10 days ago by pmarijon100
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Comment: C: Seqan read compressed stream
... And bz2 according to http://docs.seqan.de/seqan/master/group_FileCompressionTags.html#FileCompressionTags%23BgzFile ...
written 4 months ago by pmarijon100
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Comment: C: Seqan read compressed stream
... Is documented > These classes provide an API for accessing sequence files in different file formats, either compressed or uncompressed. Source : https://seqan.readthedocs.io/en/master/Tutorial/InputOutput/SequenceIO.html ...
written 4 months ago by pmarijon100
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Comment: C: Seqan read compressed stream
... I use a std::ifstream to get current position in file during seqan parsing, it's easy. But when I try my code on compressed file, seqan parsing failed. So seqan didn't detect my stream contain compressed data or seqan can't work on compressed stream, but isn't documented. ...
written 4 months ago by pmarijon100
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Comment: C: Seqan read compressed stream
... I want generate a progress bar, the post required an edit. For compress file we can have a good approximation with size of compressed file and the position in compressed file. ...
written 4 months ago by pmarijon100
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Seqan read compressed stream
... Hi, I want read a sequence file (fasta fastq bam, etc), so I read Seqan tutorial. But If I want know my position in file I need use std::ifstream (for generate a progress bar) , it's not a problem, I write this test code: ```c++ #include #include #include int main (int argc, char ** argv) { ...
seqan written 4 months ago by pmarijon100
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Comment: C: What's a good PacBio CLR read simulator?
... Thank, I read this publication, I didn't test EAGLE but they have a trouble with boost [when it's upper than 1.56](https://github.com/sequencing/EAGLE/issues/2) ...
written 15 months ago by pmarijon100
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Comment: C: What's a good PacBio CLR read simulator?
... This [issue](https://github.com/pfaucon/PBSIM-PacBio-Simulator/issues/2) explain why the build system is broken and alternative solution to build pbsim. Thank ...
written 15 months ago by pmarijon100

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Appreciated 7 days ago, created a post with more than 5 votes. For Want to use fastq-dump to download pacbio data? Read this before

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