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Old 11-09-2013, 12:32 AM   #1
zhoufan
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Location: china

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Default Can smrtpipe v2.0.1 accept both fastq and bas.h5 file

Hi,
I am using smrtanalysis 2.0.1 HybridAssembly to scafold the contigs assembled by soapdenovo.After that using P_Mapping moudle to do resequencing (Mapping all the raw data both illumina fastq reads and pacbio bas.h5 file),but the result turns out only pacbio bas.h5 mapped on the reference.
I also tried only fasta file as input to mapp to the reference using P_Mapping module ,it failed.

Is this because P_Mapping can only accept bas.h5 file?If so,how to do Resequencing step in this Circumstance?

Any suggestion would be appreciate!
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Old 11-09-2013, 08:31 PM   #2
zhoufan
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ok,reply to myself. I just find a useful tool at http://sourceforge.net/p/pb-jelly/wiki/Home/.This can fulfil my needs.
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