User: sklages

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sklages60
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Berlin, DE
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7 hours ago
Joined:
7 years, 4 months ago
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k*****@molgen.mpg.de

Posts by sklages

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Bcl2fastq conversion according to samples
... What did you get? What did you expect. There is a `[data]` section header missing. Did you try to find out what's going on from stdout output? ...
written 8 weeks ago by sklages60
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Comment: C: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... arrow works on aligned data. Maybe you should read [1] to get an idea what arrow is doing. Best, Sven [1] = https://github.com/PacificBiosciences/GenomicConsensus/blob/master/README.md ...
written 20 months ago by sklages60
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Comment: C: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... No, I don't think so. With command "create" it simply creates a XML file with all relevant infos about the BAM files. ...
written 20 months ago by sklages60
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Comment: C: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... Hi Roxane, thanks for this nice howto. That's what is missing in the PacBio docs and also in Canu docs. You could use a dataset when aligning the raw reads back to the assembly.fasta, in this case you would only need one single "pbalign" call and there would be no need to merge BAM files. data ...
written 20 months ago by sklages60
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Comment: C: Undefined reference ERROR in building the localized UCSC Genome browser with ken
... Have you solved this issue? I have a similar problem. ...
written 2.6 years ago by sklages60
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Comment: C: abyss/konnector2 : Usage Scenario
... Hi Ben, thanks for your helpful suggestions. I will try just as proposed .. :-) best, Sven ...
written 3.6 years ago by sklages60
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abyss/konnector2 : Usage Scenario
... Hi all, I am playing around "preparing" my data for shotgun assembly with abyss. I have the following data, bird genome: 2x PE libraries (500 and 1000bp) 2x LMP libraries (3kb and 10kb) All data were produced as PE100 Hiseq runs. LMP libs have been trimmed and rev-complemented with Illumina's nx ...
assembly abyss written 3.6 years ago by sklages60 • updated 3.4 years ago by jshelton0
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Comment: C: Fastq Input Data Format to abyss-pe
... ah, ok. It is now much clearer. So "lib" refers more or less to one fastq file (or pair), not necessarily to a real (sequencing) library. This is probably what has confused me :-) ...
written 3.7 years ago by sklages60
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Comment: C: Fastq Input Data Format to abyss-pe
... Thanks. Yes, it seems I have to merge (interleaved) data of the same library before assembly ... ...
written 3.7 years ago by sklages60
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Comment: C: Fastq Input Data Format to abyss-pe
... Thanks. Interesting. I do have one library on two or more HiSeq lanes; so I need to merge them first (if I want to use interleaved format) before assembling? Providing two (interleaved) files for the same library makes ABySS think these are paired-end?   ...
written 3.7 years ago by sklages60

Latest awards to sklages

Popular Question 16 months ago, created a question with more than 1,000 views. For abyss/konnector2 : Usage Scenario
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Fastq Input Data Format to abyss-pe

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