Inexperienced Question

[cambridge101]

Hello,

I have a project that requires access to an "online cancer related DNA database resource."

Unfortunately, it doesn't look like I can get access to CGHub. Would someone mind helping me? (i.e. perhaps suggest one that I can access)

Thank you!

[AntonioRFranco]

https://www.cartagenia.com

You don't mention if it should be of free access or not

[cambridge101]

AntonioRFranco - Thanks for the reply. Yes, free.

[GenoMax]

http://www.cbioportal.org/public-portal/

There are at least a couple of companies that offer different views of the TCGA data via web. Search on SeqAnswers.

[GenoMax]

http://seqanswers.com/forums/showthread.php?t=48485

http://seqanswers.com/forums/showthread.php?t=40610

[cambridge101]

GenoMax - Thanks for the reply. I probably should have mentioned the before: select ten (10) DNA sequence strings of length at least 1Mb related to a cancer gene from ten different individuals. Make sure the sequence data is in FASTQ format and stored in one file “DNA.fas”.

[GenoMax]

Now you say

You are not going to find DNA sequences in fastq format that are 1Mb in length unless you assemble them yourself preserving the Q-scores (assembly programs do not include Q-scores in final sequence).

[cambridge101]

I have a few days to work on this project. I'm lost.

[GenoMax]

Tell us more about what the entire project is about. DNA sequence is just a part of it?

[cambridge101]

GenoMax - Thanks again for your suggestions and assistance. I'm just a little reluctant to say more about this project right now. I hope you understand.

[cambridge101]

Though I don't feel I was doing anything unethical, others may disagree. Therefore, I deleted the complete requirements to avoid any conflict. Thank you.

[GenoMax]

I think you should delete the description from the post above. This appears to be a class project/home work?

Perhaps you should ask whoever assigned the project if they are certain about the fastq requirement.

[cambridge101]

Thanks for your suggestion. I don't think I'll delete it[Did decide to delete]. I don't feel that I'm doing anything unethical. I hope that it's clear that I'm not asking for anyone to complete the project for me. I'm just having a hard time finding that FASTQ data I need.

[GenoMax]

One place to look for long sequences (in fastq format) will be here: http://www.pacificbiosciences.com/ne.../publications/ I see only a couple of cancer related publication and they are from 2012 (when the reads were not as long as they are today).

If you drop the cancer requirement then you will get some really long reads here: http://blog.pacificbiosciences.com/2...d-shotgun.html They are not going to be 1Mb so you would still need to do some assembly.

[cambridge101]

One place to look for long sequences (in fastq format) will be here: http://www.pacificbiosciences.com/ne.../publications/ I see only a couple of cancer related publication and they are from 2012 (when the reads were not as long as they are today).

If you drop the cancer requirement then you will get some really long reads here: http://blog.pacificbiosciences.com/2...d-shotgun.html They are not going to be 1Mb so you would still need to do some assembly.

Thanks! I'm not sure I can drop the cancer requirement. I checked: http://www.pacificbiosciences.com/ne.../publications/ I couldn't locate the data I need.

I'm open to other suggestions if anyone has any.