Perform alignment from within R

[plger]

Use the Rbowtie (and perhaps QuasR) to reproduce our bowtie alignment from within R. This should eventually replace the current content of the alignment.R

• [ ] function to create bowtie1 indexes from a set of fasta files
• [ ] function to perform perfect end-to-end alignment with bowtie1 (input fasta, output BAM)
• eventually, but not strictly needed:
  • [ ] function to perform soft-clipped alignment with either STAR or bowtie2 -local

[dktanwar]

QuasR can perform the first 2 steps

1. bowtie1 indexes are automatically created while aligning with qAlign function.

2. For indexes, we can use the BSgenome package. If we specify the BSgenome, it will automatically be downloaded from Bioconductor[bioconductor.org] website. Or, we could provide the path to fa file for indexes. It can also accept multiple .fa files.

3. Duplicating bowtie1 options:

   • -p (no. of threads)
   • -v (report end-to-end hits w/ <=v mismatches; ignore qualities)
   • -S (write SAM format)
   • -a (report all alignments per read)
   • --best (hits guaranteed best stratum; ties broken by quality)
   • --strata (hits in sub-optimal strata aren't reported (requires --best))
   • -m (suppress all alignments if > exist (def: no limit))
   • -f (query input files are (multi-)FASTA .fa/.mfa)
   • --un (write unaligned reads/pairs to file(s) )

qAlign: Alignments are generated using the parameters -m maxHits --best --strata. This will align reads with up to “maxHits” best hits in the genome and selects one of them randomly.

4. star is also available to be used from R

install_github("flow-r/ngsflows")
library(ngsflows)

[plger]

• for building the index we might as well just use Rbowtie, since QuasR uses that (this way we can avoid the requirement for BSgenome)
• for the alignment, we do not want exactly the qAlign behavior - we need the "-a" option.

On Thu, Jun 21, 2018 at 3:47 PM, Deepak Tanwar notifications@github.com wrote:

QuasR can perform the first 2 steps

1.

bowtie1 indexes are automatically created while aligning with qAlign function. 2.

For indexes, we can use the BSgenome package. If we specify the BSgenome, it will automatically be downloaded from Bioconductor[ bioconductor.org] website. Or, we could provide the path to fa file for indexes. It can also accept multiple .fa files. 3.

Duplicating bowtie1 options:

• -p (no. of threads)
• -v (report end-to-end hits w/ <=v mismatches; ignore qualities)
• -S (write SAM format)
• -a (report all alignments per read)
• --best (hits guaranteed best stratum; ties broken by quality)
• --strata (hits in sub-optimal strata aren't reported (requires --best))
• -m (suppress all alignments if > exist (def: no limit))
• -f (query input files are (multi-)FASTA .fa/.mfa)
• --un (write unaligned reads/pairs to file(s) )

qAlign: Alignments are generated using the parameters -m maxHits --best --strata. This will align reads with up to “maxHits” best hits in the genome and selects one of them randomly.

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[dktanwar]

Hi @plger

For alignment, we can use Rsubread with the following options:

https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf

1. -B: 1000?
2. −−multiMapping

• −−allJunctions ? Do we need this?

Will this be enough for replacing both bowtie1 and STAR?

[dktanwar]

Other options suggestion:

1. How many mismatches to be allowed?

• For now: 3

[dktanwar]

Hi @plger

Are you aware of ShortStack?

What do you think about the alignment procedure?

[dktanwar]

@plger do we need this issue?

I think the alignment problem is solved with Rsubread.