Question: How To Visualize The Quality Of Sequencing Data In Colorspace (Solid) Format?
0
gravatar for Roger
7.1 years ago by
Roger0
Roger0 wrote:

Hi all,

I've a colorspace library. Everybody knows that SOLiD has low-quality ends from reads. So, I would like to know if there are one tool to check this quality graphically. Just like a dotplot of my reads quality.

For example:

csfasta 33231223214523

qual 29 32 29 9 4 6 -1

And the graphics will be:


| G | G | G | W | W | B |


G = Good W = Warning B = Bad

Any help will be greatly appreciated.

10ks

read qualitycontrol • 2.6k views
ADD COMMENTlink modified 7.1 years ago by Istvan Albert ♦♦ 85k • written 7.1 years ago by Roger0

Hi Roger. Have you tried LifeScope?

ADD REPLYlink written 7.1 years ago by Leandro Lima960

Hello Leandro Lima can you please help me with this post?

Thanks in advance.

ADD REPLYlink modified 9 months ago by RamRS30k • written 6.5 years ago by gauravdube0070

What exactly you are looking for? There are many solid based read-trimmers that you can search here on biostars. What purpose visualizing the quality of read will serve?

ADD REPLYlink written 7.1 years ago by Ashutosh Pandey12k
2
gravatar for Istvan Albert
7.1 years ago by
Istvan Albert ♦♦ 85k
University Park, USA
Istvan Albert ♦♦ 85k wrote:

Transform the reads to either color space fastq via double encoding or just decode it to FASTQ and run a FASTQ based quality control tool on it: fastqc etc.

There are some tools mentioned here: Transforming and manipulating color space reads

ADD COMMENTlink modified 7.1 years ago • written 7.1 years ago by Istvan Albert ♦♦ 85k

10ks Istvan. You're the MAN.

ADD REPLYlink written 7.1 years ago by Roger0
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