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PacBio Long Read error correction through PBcR --> pacbio.spec field

Hello,

I'm trying to self-correct PacBio long fastq sequences using Celera 8.2 assembler through the PBcR pipeline.

Since the pacbio.spec option is mandatory, can anybody explain me how a correct minimal pacbio.spec file should be built?

Thank you in advance for your help!

error-correction long-reads celera pacbio
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updated by Ram Ram • written by am • am

1 answer

The pacbio.spec file is for Celera Assemler. Here are the two example files:

Multicore machine: http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData/pacbio.spec

SGE version: http://www.cbcb.umd.edu/software/PBcR/data/sampleData/pacbio.SGE.spec

The options are well documented here.

Multiple examples are given here and here

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updated by Ram Ram • written by GouthamAtla GouthamAtla

Edit: Updated few Links.

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written by GouthamAtla GouthamAtla

From the tutorial do you have any idea about the -l parameter;

% <wgs>/<Linux-amd64>/bin/PBcR -length 500 -partitions 200 -l lambdaIll -s pacbio.spec -fastq pacbio.filtered_subreads.fastq genomeSize=50000 illumina.frg

I think it just give a name to result but for example when I want to direct the output to different directory it does not work;

% <wgs>/<Linux-amd64>/bin/PBcR -length 500 -partitions 200 -l /home/user/test/lambdaIll -s pacbio.spec -fastq pacbio.filtered_subreads.fastq genomeSize=50000 illumina.frg

Any idea?

I tried PBcR --help but there is no info about it is there any will documented information about the software?

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updated by Ram Ram • written by Medhat Medhat

Thats the library name. Not the Path.

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written by GouthamAtla GouthamAtla

So how can I direct the output to the path I want?

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updated by Ram Ram • written by Medhat Medhat

It will not work and give you the message can not create temp/"the path you want"

Generally I found a work around that just run the command from the place you want your output to be, but I do not think that it is logical or even good idea that is why I asked :D

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updated by Ram Ram • written by Medhat Medhat

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