User: chacazoulou

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Posts by chacazoulou

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Answer: A: khmer-2.0 normalize-by-median.py fails to recognise paired reads
... Alright, it's solved. Thanks again for your support genomax2 (and the reformating of my messages, couldn't get that right). Basically, it was not an issue with the input files (which is probably why I was I puzzled, to say the least), but with the way that I was calling the normalize-by-median.py s ...
written 2.1 years ago by chacazoulou0
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Comment: C: khmer-2.0 normalize-by-median.py fails to recognise paired reads
... thanks for the reply, I get the error from the beginning of normalize-by-mean.py ; it doesn't seem to process any read. (the error meassage cited in my original post is the first piece of log that is prompted) I doubt that the trimmed data contains orphaned reads or has headers in a format that is ...
written 2.1 years ago by chacazoulou0 • updated 2.1 years ago by genomax59k
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Comment: C: khmer-2.0 normalize-by-median.py fails to recognise paired reads
... Hi, yes I use interleaved reads, but that's what's recommended for khmer (http://khmer-protocols.readthedocs.io/en/v0.8.2/mrnaseq/1-quality.html , @ adaptors trimming step). Also, there's only one input file possible, so I don't believe that independent could even be specified. ...
written 2.1 years ago by chacazoulou0
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khmer-2.0 normalize-by-median.py fails to recognise paired reads
... Dear all, I'm transitioning from khmer-0.7.1 to khmer-2.0 and my pipepline (PE Illumina raw reads->Trimomatic->interleave-reads.py->extract-paired-reads.py->normalize-by-mean.py) fails to recognise the reads as paired reads at the digital normalization step, as suggested by the following ...
software error alignment next-gen sequencing written 2.1 years ago by chacazoulou0

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