determine what best alignment tool when using R on fastq files?
1
0
Entering edit mode
3.5 years ago

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 ?

R alignment RNA-Seq fastq • 2.1k views
ADD COMMENT
1
Entering edit mode

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 REPLY
1
Entering edit mode

You pretty much said what I wanted to write :)

ADD REPLY
0
Entering edit mode

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 REPLY
1
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
2
Entering edit mode
3.5 years ago
mastal511 ★ 2.1k

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 2329 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6