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Forum: Bioinformatics 12-21-2015, 09:52 PM
Replies: 2
Views: 6,792
Posted By Benh
A bit late to this thread... ANNOVAR extracted...

A bit late to this thread...
ANNOVAR extracted these conservation scores from dbNSFP and not from UCSC which could have positive and negative value.
Forum: Bioinformatics 09-03-2014, 10:42 AM
Replies: 3
Views: 7,413
Posted By Benh
Thank you for your response Tommy. Indeed I...

Thank you for your response Tommy.

Indeed I have read both articles (actually it's the same paper that I posted), but it seems to me that there is no clear benefit why TPM is better... Simply...
Forum: Bioinformatics 09-03-2014, 09:46 AM
Replies: 3
Views: 7,413
Posted By Benh
TPM vs RPKM

Hello SeqAns community,

This may be a naive question, but after reading the paper (http://lynchlab.uchicago.edu/publications/Wagner,%20Kin,%20and%20Lynch%20(2012).pdf)from Wagner, 2012 and...
Forum: 454 Pyrosequencing 05-09-2013, 08:53 AM
Replies: 21
Views: 9,695
Posted By Benh
!!! I see what you mean now. Sorry I've been...

!!!

I see what you mean now. Sorry I've been reading the post with my Lib-L beer goggles :D

Well, I'm glad that at least your problem seem to be sample specific. Thanks for sharing your...
Forum: 454 Pyrosequencing 05-08-2013, 09:40 PM
Replies: 21
Views: 9,695
Posted By Benh
Thanks for the reply ajthomas! If I...

Thanks for the reply ajthomas!

If I understand your case correctly, it is actually normal to see only one amplification primer (amp. B sequence) but not A sequence+key because of where sequencing...
Forum: 454 Pyrosequencing 05-07-2013, 03:01 AM
Replies: 21
Views: 9,695
Posted By Benh
Hi all, I'm wondering if other labs are...

Hi all,

I'm wondering if other labs are having problem 5) mentioned in the original post about high trimming rates and short reads.

Probably since early 2013 many of our amplicons/16s...
Forum: 454 Pyrosequencing 03-19-2013, 07:17 AM
Replies: 2
Views: 2,177
Posted By Benh
Thanks for sharing your experience!

Thanks for sharing your experience!
Forum: 454 Pyrosequencing 03-15-2013, 01:44 AM
Replies: 2
Views: 2,177
Posted By Benh
running ssDNA on RNA chip

Hi all,

This might be an old question, but I'm wondering if anybody know how would ssDNA run on a RNA bioanalyzer chip? Do ssDNA migrate at a similar speed as RNA?

The closest post I've found...
Forum: 454 Pyrosequencing 03-15-2013, 01:40 AM
Replies: 5
Views: 2,283
Posted By Benh
Hi jdelton, Do you mind sharing what's your...

Hi jdelton,

Do you mind sharing what's your typical recovery from ampure and gel purification?

When we follow Roche's clean up protocol our recovery is super below like under 10% (even <1%). It...
Forum: 454 Pyrosequencing 08-31-2012, 10:22 AM
Replies: 3
Views: 3,008
Posted By Benh
Hi ngseq, not sure if you have solved your...

Hi ngseq, not sure if you have solved your problem yet... but likely the source for the high mw smear is from the fragmented DNA template that got carried over from PCR. In which case gel...
Forum: Sample Prep / Library Generation 08-31-2012, 10:11 AM
Replies: 1
Views: 1,574
Posted By Benh
We have a S220 in our lab for ~2 yrs and it works...

We have a S220 in our lab for ~2 yrs and it works like a charm. No service needed so far to my knowledge.
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