[Bioc-devel] Question about external algorithms to Bioconductor package

[Ioannis Vardaxis]

First I create the index using:

buildindex(basename=¡°Rsubread_index¡±,reference=¡°/path/to/hg19.fa",colorspace=FALSE)

Where hg19.fa is the fasta file with the chromosomes, chr1 etc.

Then I run:

                                 align( index=¡°/path/to/Rsubread_index¡±,readfile1=¡°/path/to/reads.fastq¡±,type=¡°dna¡±,output_format=¡°BAM¡±,
output_file=¡°/path/to/output.bam¡±,maxMismatches=1,unique=TRUE,indels=0)

I have short reads from hg19. And I want to map them with at most 1 mismatch and keep the uniquely mapped only. Therefore I set indels=0. From that I get zero occurrences. Rbowtie maps 73% on the other hand.

Thanks for the help!


--
Ioannis Vardaxis
Stipendiat IMF
NTNU

From: Wei Shi <shi at wehi.edu.au<mailto:shi at wehi.edu.au>>
Date: Sunday, 26 November 2017 at 23:08
To: Ioannis Vardaxis <ioannis.vardaxis at ntnu.no<mailto:ioannis.vardaxis at ntnu.no>>, Martin Morgan <martin.morgan at roswellpark.org<mailto:martin.morgan at roswellpark.org>>
Cc: "A.E.S." <adrian.salatino at conicet.gov.ar<mailto:adrian.salatino at conicet.gov.ar>>, Ryan Thompson <rct at thompsonclan.org<mailto:rct at thompsonclan.org>>, "bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>" <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
Subject: Re: [Bioc-devel] Question about external algorithms to Bioconductor package

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.vardaxis at ntnu.no<mailto:ioannis.vardaxis at ntnu.no>>
Date: Sunday, November 26, 2017 at 9:30 PM
To: Martin Morgan <martin.morgan at roswellpark.org<mailto:martin.morgan at roswellpark.org>>
Cc: "A.E.S." <adrian.salatino at conicet.gov.ar<mailto:adrian.salatino at conicet.gov.ar>>, Ryan Thompson <rct at thompsonclan.org<mailto:rct at thompsonclan.org>>, "bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>" <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>, Wei Shi <shi at wehi.edu.au<mailto:shi at 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.morgan at roswellpark.org<mailto:martin.morgan at 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 don©öt see any reason
using it, and this is a big problem if I cannot use bowtie inside a
bioconductor package.
Thanks


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