problem with newbler(error)
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Entering edit mode
6.9 years ago
midox ▴ 290

hello,
I have a problem with Newbler.
I launched the command to try an assembly of two .fq files but here the error.
 

Created assembly project directory /home/mido/test_Newbler/projet2
2 read files successfully added.
    sim.p1.fq  (Fastq paired-end dataset, with standard scores)
    sim.p2.fq  (Fastq paired-end dataset, with standard scores)
Assembly computation starting at: Thu Jun 25 10:49:51 2015  (v2.9 (20130529_1641))
Indexing sim.p1.fq (with quality scores)...

  -> 3500 reads, 350000 bases.
Indexing sim.p2.fq (with quality scores)...

  -> 3500 reads, 350000 bases.
Error:  At least one read sequence must be present in the project
        in order to proceed with mapping or assembly.
sequencing Assembly newbler • 1.5k views
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Entering edit mode
6.9 years ago
lexnederbragt ★ 1.3k

Newbler will first look for low quality regions and trim them off. What may have happened is that Newbler trimmed all the bases of your reads. I assume there will be a 454TrimSatus.txt file, which shows the original read length and trimmed read length for each read. Perhaps your quality scores are all very low?

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