You got to be aware that Rbowtie/bowtie does not detect indels and quite often this is needed for the analysis of DNA sequencing data. Bowtie is probably the only aligner that does not detect indels.
As I mentioned in my last email, I would be happy to take a look at why Rsubread is slow if you can provide your command and screen output. But there are certainly other Bioconductor packages that can do proper alignment for you. Wei -------------------- Wei Shi, PhD Laboratory Head The Walter and Eliza Hall Institute of Medical Research Melbourne, Australia From: Ioannis Vardaxis <ioannis.varda...@ntnu.no> Date: Sunday, November 26, 2017 at 9:30 PM To: Martin Morgan <martin.mor...@roswellpark.org> Cc: "A.E.S." <adrian.salat...@conicet.gov.ar>, Ryan Thompson <r...@thompsonclan.org>, "bioc-devel@r-project.org" <bioc-devel@r-project.org>, Wei Shi <s...@wehi.edu.au> Subject: Re: [Bioc-devel] Question about external algorithms to Bioconductor package I used Rbowtie and the mapping was done in 7 minutes, the results where fine too. Rsubread had been running for 2 days so I had to stop it. But anyway I can use Rbowtie which is nice :) Ioannis Vardaxis Stipendiat NTNU Sendt fra min iPhone 26. nov. 2017 kl. 04:14 skrev Martin Morgan <martin.mor...@roswellpark.org<mailto:martin.mor...@roswellpark.org>>: I think that generally Rsubread is 'fast' so you might make sure that there are not obvious problems, e.g., aligning reads to the wrong reference; maybe Wei Shi will chime in. Martin On 11/24/2017 09:57 AM, Ioannis Vardaxis wrote: Hi, I tried the Rsubread package you suggested and the mapping is running. However it takes like forever to end. Even in parallel it needs some days to run while bowtie for example needs only a couple of hours in 4 cores. Is there any way of speeding up Rsubread? Or else I don¹t see any reason using it, and this is a big problem if I cannot use bowtie inside a bioconductor package. Thanks This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
