Question: Tools to view fastq file
2
gravatar for Roden Luo
3.5 years ago by
Roden Luo20
United States
Roden Luo20 wrote:

Hi ~, I am curious about whether there is a tool for us to VIEW fastq file(NGS raw data). Like IGV, we can view sam/bam files to get some insights or check the results. So what I am looking for is a tool that can show the sequences and qualities of a small number of reads(e.g. less than 20). My idea is to use the brightness/depth of color to show the qualities. What's more, I hope I can drag the reads to align/compare them with each other in order to get some insight from doing so.

I have searched on google by keywords "(the best) tool to see/view fastq". But all the results are related to the processing of fastq files, NOT VIEWING.

So, is there a tool for that? If not, anyone has the same need as I do? Is it worthy to develop one?

Many thanks, Roden

tool fastq • 16k views
ADD COMMENTlink modified 2.6 years ago by nora40 • written 3.5 years ago by Roden Luo20

Hi:

fastq files are normally just sequences without the information where in the genome they align - so IGV and other genome browsers cannot really reperesent it accurately

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Michi950

Yeah, so what I am looking is a little bit like: IGV without reference, and I can even drag(e.g. horizontally or vertically) the reads to align manually.

Also like: I want to align/assemble about 20 reads in fastq format MANUALLY and see the results. Because I think if the amount of reads is not so huge, I can do it by my self and compare it to the results from other tools. But I do not want to do it by pen and paper.

ADD REPLYlink written 3.5 years ago by Roden Luo20

umm not sure that a tool like that exists. Maybe because just running a classic assembler for Sanger sequences or maybe Velvet, spades or ssaha should be enough. Later you could align you sequences to the assembly and watch the alignments with IGV.

ADD REPLYlink written 3.5 years ago by cpcantalapiedra140
3
gravatar for openpaul
2.6 years ago by
openpaul30
openpaul30 wrote:

If you really just want to have a quick glance at your data, have a look into fqless: https://github.com/openpaul/fqless

I wrote this small piece of software as I wanted to peak into sequencing reads without much hassle. It actually does color code the reads as you suggested, but you can not interact with anything. Just observe.

ADD COMMENTlink written 2.6 years ago by openpaul30
1

For the job it does, this is really great - nice one :)

ADD REPLYlink written 2.6 years ago by John12k
0
gravatar for Benn
3.5 years ago by
Benn7.9k
Netherlands
Benn7.9k wrote:

You can use fastQC tool to see the quality of your reads.

If you want to look at the raw data, use a text editor or the bash command line

head file.fastq

or

cat file.fastq
ADD COMMENTlink written 3.5 years ago by Benn7.9k

Thank you b.nota!

Sorry I did not make it clear. I knew that I could head or cat and see the plain-text style of the reads. But what I am looking is to VIEW vividly. Like IGV without reference, and I can even drag(e.g. horizontally or vertically) the reads to align manually.

ADD REPLYlink written 3.5 years ago by Roden Luo20

So something like:

head -n40 file.fq | fq2fa - | muscle -in - -out pointlessAlignment.fa
ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by 5heikki8.6k
0
gravatar for Michael Dondrup
3.5 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

There are some GUI tools mostly for windows, like this one http://www.dnabaser.com/download/nextgen-fastq-editor/ which maybe allow for some individual interaction.

ADD COMMENTlink written 3.5 years ago by Michael Dondrup46k

I am going to try and give some feedbacks. Thank you Michael!

ADD REPLYlink written 3.5 years ago by Roden Luo20
0
gravatar for Nari
3.5 years ago by
Nari870
United States
Nari870 wrote:

Geneious on trial version.

ADD COMMENTlink written 3.5 years ago by Nari870
0
gravatar for nora
2.6 years ago by
nora40
algeria
nora40 wrote:

try with wordpad to to observe the contents of fastq

ADD COMMENTlink written 2.6 years ago by nora40
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