determine what best alignment tool when using R on fastq files?

Question

[emadelhewihy]

is there function used in alignment on fastq file , or using alignment tools is better ? and what is the tool or function to do that ?

[WouterDeCoster]

Ehm, you'll need to explain a bit more what you are doing, but I'm 99% sure you need an alignment tool and R is not appropriate for your project.

[Kevin Blighe]

You pretty much said what I wanted to write :)

[emadelhewihy]

sot exactly what you said is true, i have DNA_sqe on big fastq size, and have another sequence want to be alignment it with the sequences in the fastq file .... so what pacjages can use in R to do the alignment process?

[Kevin Blighe]

Are you really limited to using just R? Do you only have a Windows OS?

R is tailoured for downstream data analysis due to limits in its very architecture, mainly in terms of memory. R has recently acquired many functions that are parallel-process enabled, though.

It is possible to make system calls from R but these then still require non-R programs to do alignment.

Take a look at this old thread (and I agree wholeheartedly with Devon and Sean): NGS DNA-seq analysis packages for mapping, calling cariants, annotation on R / bioconductor

[WouterDeCoster]

The only R package I am aware of is Rsubread https://bioconductor.org/packages/release/bioc/html/Rsubread.html

But the best tool for your project is likely not accessible through R.

Answer 1

[mastal511]

Use alignment tools - there are various aligners - bwa, bowtie, BBMap.

[emadelhewihy]

bwa, bowtie, BBMap. > what are those ? are they R packages!!

[Kevin Blighe]

They are non-R, compiled programs that require UNIX, linux, or MAC. They perform re-alignment of FASTQ / FASTA files to a reference genome.