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

Question

[am]

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!

Answer 1

[GouthamAtla]

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

[GouthamAtla]

Edit: Updated few Links.

[Medhat]

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?

[GouthamAtla]

Thats the library name. Not the Path.

[Medhat]

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

[GouthamAtla]

I do not see any option for that. http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR

Whats the error when you give path to -l?

[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