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PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study
BSD 3-Clause Clear License
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can not find makePbi #7

Closed wyim-pgl closed 8 years ago

wyim-pgl commented 8 years ago

Dear team FALCON,

I am trying to find makePbi.py but I can't.

Where can I get it?

Thank you.

Won

wyim-pgl commented 8 years ago

Is there anyway to run without SMRTanalysis 3.0?

pb-jchin commented 8 years ago

well. it is not trivial to do the "augmented alignment" without PacBio read BAM support, so your best bet is to move to 3.0. Also, in the official 3.0 release, the makePBI.py is no longer needed, if you use the latest master head, the line is commented out. (You can commented it out yourself.)

wyim-pgl commented 8 years ago

Oh.

Happy new year first.

where can i find SMRTanalysis 3.0?

Won

-------- Original message -------- From: Jason Chin notifications@github.com Date: 1/1/2016 17:10 (GMT-08:00) To: PacificBiosciences/FALCON_unzip FALCON_unzip@noreply.github.com Cc: Won C Yim wyim@unr.edu Subject: Re: [FALCON_unzip] can not find makePbi (#7)

well. it is not trivial to do the "augmented alignment" without PacBio read BAM support, so your best bet is to move to 3.0. Also, in the official 3.0 release, the makePBI.py is no longer needed, if you use the latest master head, the line is commented out. (You can commented it out yourself.)

— Reply to this email directly or view it on GitHub[github.com]https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_PacificBiosciences_FALCON-5Funzip_issues_7-23issuecomment-2D168354200&d=BQMCaQ&c=jifKnBYnyVBhk1h9O3AIXsy5wsgdpA1H51b0r9C8Lig&r=Sntc2dkdJe9SrXxKO-MUvw&m=uJ-iCjYKxFBhA9i-JA9so036Qx9eYIEuiJr1jS99Nu0&s=mBMPD2xNBtvjd_mz7uYoAe1xeJcPXaTzxdadLn-tnsM&e=.

pb-jchin commented 8 years ago

please contact PacBio TechSupport for the official release.

wyim-pgl commented 8 years ago

i think i didn't released yet.

I will contact!

-------- Original message -------- From: Jason Chin notifications@github.com Date: 1/1/2016 17:45 (GMT-08:00) To: PacificBiosciences/FALCON_unzip FALCON_unzip@noreply.github.com Cc: Won C Yim wyim@unr.edu Subject: Re: [FALCON_unzip] can not find makePbi (#7)

please contact PacBio TechSupport for the official release.

— Reply to this email directly or view it on GitHub[github.com]https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_PacificBiosciences_FALCON-5Funzip_issues_7-23issuecomment-2D168355454&d=BQMCaQ&c=jifKnBYnyVBhk1h9O3AIXsy5wsgdpA1H51b0r9C8Lig&r=Sntc2dkdJe9SrXxKO-MUvw&m=biPR9X1cCHnv3e_b0a17yZymYdeC1nej0KMhICBf644&s=7kPIT_IrzqNmSnXZQxA2npWjkT1BDFfRfIYxbUZs9iY&e=.

wyim-pgl commented 8 years ago

Hmm, is there anyway to use 2.3 instead of 3.0?

pb-jchin commented 8 years ago

It needs the support of storing reads in BAM files which is the new feature of 3.0.

wyim-pgl commented 8 years ago

hmmm...

We really want it to use for our tetraploidy genome.

pb-cdunn commented 8 years ago

Hopefully you were able to upgrade to 3.0.