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
