Rsubread for paired end SOLID sequencing

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Simon Coetzee ▴ 50

@simon-coetzee-5051

Last seen 2.5 years ago

USA Cedars-Sinai Medical Center

I have some paired end SOLID sequencing data, the protocol using F3/F5 fragments (not the simpler F3/R3). Both fragments come from the same strand. Some of the nuances are explained here: http://www.biostars.org/p/48597/ Having read the manual for Rsubread, its clear that it can handle SOLID sequencing, colorspace reads, and paired end sequencing. However, is the F3/F5 protocol directly supported, or will there have to be preprocessing of the F5 fragments? Simon Coetzee -- Centro Regional de Hemoterapia Hospital das ClÃnicas da Faculdade de Medicina de *RibeirÃ£o Preto *Universidade de SÃ£o Paulo -- No trees were killed to send this message, but a large number of electrons were terribly inconvenienced. [[alternative HTML version deleted]]

Sequencing Rsubread Sequencing Rsubread • 1.4k views

ADD COMMENT • link updated 11.4 years ago by Wei Shi ★ 3.6k • written 11.5 years ago by Simon Coetzee ▴ 50

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Wei Shi ★ 3.6k

@wei-shi-2183

Last seen 18 days ago

Australia/Melbourne

Dear Simon, Yes, the F3/F5 protocol is supported by Subread. You will need to set PE_orientation="ff" when you run align or subjunc functions. This will tell the alignment programs that the two reads from the same pair are on the same strand and they can then be handled properly. Sorry the documentation did not provide enough details about how to map such reads. I have just added more descriptions to this to the help pages and user guide to make them more clearer. Best wishes, Wei On Jul 27, 2013, at 6:31 AM, Simon Coetzee wrote: > I have some paired end SOLID sequencing data, the protocol using F3/F5 > fragments (not the simpler F3/R3). Both fragments come from the same > strand. Some of the nuances are explained here: > http://www.biostars.org/p/48597/ > > Having read the manual for Rsubread, its clear that it can handle SOLID > sequencing, colorspace reads, and paired end sequencing. However, is the > F3/F5 protocol directly supported, or will there have to be preprocessing > of the F5 fragments? > > Simon Coetzee > -- > Centro Regional de Hemoterapia > Hospital das Cl?nicas da Faculdade de Medicina de *Ribeir?o Preto > *Universidade de S?o Paulo > > -- > > No trees were killed to send this message, but a large number of electrons > were terribly inconvenienced. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}

ADD COMMENT • link 11.4 years ago Wei Shi ★ 3.6k

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Thanks for the help, everything is running smoothly now. Only one more question, is there an option in Rsubread equivalent to "-b" in Subread (to output the sam file in basespace format, when starting from colorspace fasta)? Thanks again, Simon Coetzee Centro Regional de Hemoterapia Hospital das ClÃnicas da Faculdade de Medicina de RibeirÃ£o Preto Universidade de SÃ£o Paulo On Fri, Jul 26, 2013 at 11:20 PM, Wei Shi <shi@wehi.edu.au> wrote: > Dear Simon, > > Yes, the F3/F5 protocol is supported by Subread. You will need to set > PE_orientation="ff" when you run align or subjunc functions. This will tell > the alignment programs that the two reads from the same pair are on the > same strand and they can then be handled properly. > > Sorry the documentation did not provide enough details about how to map > such reads. I have just added more descriptions to this to the help pages > and user guide to make them more clearer. > > Best wishes, > > Wei > > On Jul 27, 2013, at 6:31 AM, Simon Coetzee wrote: > > > I have some paired end SOLID sequencing data, the protocol using F3/F5 > > fragments (not the simpler F3/R3). Both fragments come from the same > > strand. Some of the nuances are explained here: > > http://www.biostars.org/p/48597/ > > > > Having read the manual for Rsubread, its clear that it can handle SOLID > > sequencing, colorspace reads, and paired end sequencing. However, is the > > F3/F5 protocol directly supported, or will there have to be preprocessing > > of the F5 fragments? > > > > Simon Coetzee > > -- > > Centro Regional de Hemoterapia > > Hospital das ClÃnicas da Faculdade de Medicina de *RibeirÃ£o Preto > > *Universidade de SÃ£o Paulo > > > > -- > > > > No trees were killed to send this message, but a large number of > electrons > > were terribly inconvenienced. > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:17}}

ADD REPLY • link 11.4 years ago Simon Coetzee ▴ 50

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Hi Simon, I have just added 'color2base' option to the align function in Rsubread to let it access the color base conversion facility in Subread (-b option). I have committed it to the devel branch of Rsubread (v1.11.9) and it should be available to you in a couple of days. Thanks, Wei On Jul 30, 2013, at 6:11 AM, Simon Coetzee wrote: > Thanks for the help, everything is running smoothly now. > Only one more question, is there an option in Rsubread equivalent to "-b" in Subread (to output the sam file in basespace format, when starting from colorspace fasta)? > > Thanks again, > > Simon Coetzee > > Centro Regional de Hemoterapia > Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto > Universidade de São Paulo > > > > On Fri, Jul 26, 2013 at 11:20 PM, Wei Shi <shi@wehi.edu.au> wrote: > Dear Simon, > > Yes, the F3/F5 protocol is supported by Subread. You will need to set PE_orientation="ff" when you run align or subjunc functions. This will tell the alignment programs that the two reads from the same pair are on the same strand and they can then be handled properly. > > Sorry the documentation did not provide enough details about how to map such reads. I have just added more descriptions to this to the help pages and user guide to make them more clearer. > > Best wishes, > > Wei > > On Jul 27, 2013, at 6:31 AM, Simon Coetzee wrote: > > > I have some paired end SOLID sequencing data, the protocol using F3/F5 > > fragments (not the simpler F3/R3). Both fragments come from the same > > strand. Some of the nuances are explained here: > > http://www.biostars.org/p/48597/ > > > > Having read the manual for Rsubread, its clear that it can handle SOLID > > sequencing, colorspace reads, and paired end sequencing. However, is the > > F3/F5 protocol directly supported, or will there have to be preprocessing > > of the F5 fragments? > > > > Simon Coetzee > > -- > > Centro Regional de Hemoterapia > > Hospital das Clínicas da Faculdade de Medicina de *Ribeirão Preto > > *Universidade de São Paulo > > > > -- > > > > No trees were killed to send this message, but a large number of electrons > > were terribly inconvenienced. > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:22}}

ADD REPLY • link 11.4 years ago Wei Shi ★ 3.6k

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