User: mjhsieh

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mjhsieh0
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Posts by mjhsieh

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Answer: A: FASTQC and PacBio reads
... Please start from the bax.h5 files instead of the fastq files. You can find the documents here https://github.com/PacificBiosciences/SMRT-Analysis/wiki/Official-Documentation and here https://github.com/PacificBiosciences/Bioinformatics-Training/wiki . Also look into the HGAP assembly method / proto ...
written 3.6 years ago by mjhsieh0
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Comment: C: Install HGAP for de novo PacBio Assembly
... I only answered the installation question, not trying to design your experiments. The 10TB of space is an anticipation of data size for a generally big project, not software installation. You will need to have a linux virtual machine on your machine for very small pilot testings. And then start to l ...
written 3.6 years ago by mjhsieh0
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Answer: A: Install HGAP for de novo PacBio Assembly
... For more information, you can start from this page. http://www.pacb.com/devnet/ ...
written 3.6 years ago by mjhsieh0
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Answer: A: Install HGAP for de novo PacBio Assembly
... $ du -sh smrtanalysis* 179M    smrtanalysis-patch_2.3.0.140936.p4.run 4.0K    smrtanalysis-patch_2.3.0.140936.p4.run.md5 1.1G    smrtanalysis_2.3.0.140936.run 4.0K    smrtanalysis_2.3.0.140936.run.md5 Not 1TB. ...
written 3.6 years ago by mjhsieh0
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Answer: A: How to get InterPulse Duration (IPD) data from PacBio?
... Have you tried this? http://files.pacb.com/software/instrument/2.0.0/bas.h5%20Reference%20Guide.pdf ...
written 3.6 years ago by mjhsieh0
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Answer: A: Pacbio: Extract h5 file and Filter sequences and compress it to h5 file.
... pbh5tools is what you need. ...
written 3.6 years ago by mjhsieh0

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