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Old 02-28-2019, 04:09 AM   #1
DeanT
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Location: United Kingdom

Join Date: Feb 2019
Posts: 2
Post Hello!

Hi everyone,

I'm Dean, a first year PhD student embarking on a three year Bioinformatics project. My project primarily involves processing & analysing methylation data derived using Microarray & Whole Genome Bisulfite Sequencing

Learning Bioinformatics is no easy task, and I have joined so I can learn from the wider sequencing community. Hopefully, as I get more experienced, I will be able give advice back to members in the future!

Fingers crossed,

Dean
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Old 03-19-2019, 01:03 AM   #2
AliV
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Location: Netherlands

Join Date: Feb 2019
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Hi Dean,

I have a question for you in regard to bisulfite conversion and sequencing. My question is not so much related to dry lab portion, rather to wet lab. May I ask what kind of protocol you use? One of the problems that we encounter is that we must sequence a lot to get the desired depth of 30X, though our sample complexity is good enough to have low duplication rate. So, I am looking for an optimized procedure. Would it be possible for you to share your protocol with us?

Thank you in advance and looking to hear from you!

Cheers,
Ali
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Old 03-25-2019, 01:01 AM   #3
blake luby
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Location: tyler,tx

Join Date: Mar 2019
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hello friend, i'm blake luby from tyler tx
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Old 04-09-2019, 12:08 AM   #4
DeanT
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Location: United Kingdom

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Hi Ali. Sorry for the late reply!

Unfortunately my research will solely be focusing on the dry lab work (Bioinformatics), so I am unable to answer your question.

It is worth noting that depending on protocol (library kit, sequencing technique), the degree and type of trimming during QC also changes. For example, it is not recommended that deduplication is performed if working with RRBS. In fact, different library prep kits require tailored trimming protocols, and there doesn't seem to one standout method just yet.

If you do find the answer to your question, please share!

Dean
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