Re: [Bioc-devel] From Biostring matching to short read mapping

Date: Fri, 8 Nov 2019 18:19:27 + From: "Pages, Herve" To: "Bhagwat, Aditya" , "bioc-devel@r-project.org" Subject: Re: [Bioc-devel] From Biostring matching to short read mapping Message-ID: <84550bd2-9ded-04a

Re: [Bioc-devel] From Biostring matching to short read mapping

Thank you Wei, I actually love Rsubread, and use it with much appreciation on RNAseq projects, thank you for its creation :-) Cheers, Aditya From: Wei Shi [s...@wehi.edu.au] Sent: Saturday, November 09, 2019 12:02 PM To: Bhagwat, Aditya; Pages, Herve;

Re: [Bioc-devel] From Biostring matching to short read mapping

mosomes in smaller pieces. H. > > Cheers, > -Eric > > > > > Date: Fri, 8 Nov 2019 18:19:27 + > From: "Pages, Herve" > To: "Bhagwat, Aditya" , > "bioc-devel@r-project.org" > Subject: Re

Re: [Bioc-devel] From Biostring matching to short read mapping

Date: Fri, 8 Nov 2019 18:19:27 + From: "Pages, Herve" To: "Bhagwat, Aditya" , "bioc-devel@r-project.org" Subject: Re: [Bioc-devel] From Biostring matching to short read mapping Message-ID: <84550bd2-9ded-04a3-6ef6-52746c66f...@

Re: [Bioc-devel] From Biostring matching to short read mapping

Hi Aditya, Yes you are correct that Subread reports no more than 16 alignments per reads. One reason for this limitation is because subread detects indels in the read (Bowtie does not detect indels) and it has to set a limit on the number of candidate locations being considered due to the

Re: [Bioc-devel] From Biostring matching to short read mapping

Thankyou Michael, I got Rbowtie working, now functionalizing it for use within multicrispr. I noticed that in QuasR, you actually create a package with bowtie indices which you then use for future purposes. Interesting workflow, think I will make use of that functionality. Thankyou Herve. Yes,

Re: [Bioc-devel] From Biostring matching to short read mapping

Hi Aditya, Should not be too hard to parallelize. With some gotchas: using one worker per chromosome (which is the easy way to go) wouldn't be optimal because of the size differences between the chromosomes. So a better approach is to try to give each worker the same amount of work by

[Bioc-devel] From Biostring matching to short read mapping

Dear bioc-devel, multicrispr provides functions for Crispr/Cas9 gRNA design (and is being prepared for BioC). One task involves finding all genomic (mis)matches of a 23-bp candidate Cas9 sequence. Currently this is done with