Question: determine what best alignment tool when using R on fastq files?
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gravatar for emadelhewihy
18 months ago by
emadelhewihy0 wrote:

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 ?

rna-seq alignment fastq R • 973 views
ADD COMMENTlink modified 18 months ago by mastal5112.0k • written 18 months ago by emadelhewihy0
1

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.

ADD REPLYlink written 18 months ago by WouterDeCoster40k
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You pretty much said what I wanted to write :)

ADD REPLYlink written 18 months ago by Kevin Blighe47k

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?

ADD REPLYlink written 18 months ago by emadelhewihy0
1

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

ADD REPLYlink written 18 months ago by Kevin Blighe47k

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.

ADD REPLYlink written 18 months ago by WouterDeCoster40k
2
gravatar for mastal511
18 months ago by
mastal5112.0k
mastal5112.0k wrote:

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

ADD COMMENTlink written 18 months ago by mastal5112.0k

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

ADD REPLYlink written 18 months ago by emadelhewihy0

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

ADD REPLYlink written 18 months ago by Kevin Blighe47k
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