Question: paired-end sequencing or ChIA-PET
0
gravatar for fansgeng
3.4 years ago by
fansgeng0
Australia
fansgeng0 wrote:

I want to look at original ChIA-PET datasets (FASTQ). It's a kind of paired-end sequencing. The same identifier has two paired sequences. Is there any tutorial on analyzing paired-end sequences? I'm a beginner on this. I don't know how to start this? Could anyone give me some suggestions?

A little more specific, I have two fastq files,  1.fastq and 2.fastq. each PET contains a tag and half linker. I suppose I need to remove half linker sequences first. I have an vague idea that the file also contains sequence quality. What tool can I use to get the quality for each PET? How do I calculate the quality for each PET?

 

Thanks a lot!

Michael

assembly chip-seq • 1.1k views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by fansgeng0
0
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

The tools that you will most likely want to use are not yet wrapped for Galaxy.

....That I can find in the Tool Shed, however you can look through the list of public servers to double check if any have a specialty with this type of analysis: http://wiki.galaxyproject.org/PublicGalaxyServers

The protocol used by the ENCODE project hosted at UCSC http://genome.ucsc.edu may be a helpful resource. It includes methods and tools. Go into the hg19 genome browser and examine the track "GIS ChIA-PET".

Sorry that I could not personally help more, but others may see this post and be able to offer additional advice.

Best, Jen, Galaxy team

ADD COMMENTlink written 3.4 years ago by Jennifer Hillman Jackson24k
0
gravatar for fansgeng
3.4 years ago by
fansgeng0
Australia
fansgeng0 wrote:

Thanks very much for your response, Jennifer. I know that ChIA-PET track at UCSC genome browser. I just want to do some analysis from scratch. I'll have a look at the public servers.

Cheers, Michael

ADD COMMENTlink written 3.4 years ago by fansgeng0
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