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Question: paired-end sequencing or ChIA-PET
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gravatar for fansgeng
4.1 years ago by
fansgeng • 0
Australia
fansgeng • 0 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 • 1.3k views
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modified 4.1 years ago • written 4.1 years ago by fansgeng • 0
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gravatar for Jennifer Hillman Jackson
4.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for fansgeng
4.1 years ago by
fansgeng • 0
Australia
fansgeng • 0 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 COMMENT • link written 4.1 years ago by fansgeng • 0
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