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Forum: Sample Prep / Library Generation 08-01-2014, 05:38 AM
Replies: 5
Views: 2,074
Posted By ELoomis
What does your nanodrop trace look like? Low...

What does your nanodrop trace look like? Low 260/230 could mean phenol in your samples (Trizol is ~50% phenol). Check out this link for a good guide to understanding nanodrop reports (scroll down for...
Forum: Pacific Biosciences 03-28-2013, 09:03 AM
Replies: 7
Views: 8,001
Posted By ELoomis
"Problem" is relative. You'll have a harder time...

"Problem" is relative. You'll have a harder time calling the exact number of nt's in the homopolymer run, but polymerase keeps running through it, so you can still get accuracy improvement with CCS...
Forum: Pacific Biosciences 03-26-2013, 10:47 PM
Replies: 7
Views: 8,001
Posted By ELoomis
Indeed. The measured signal is based on the...

Indeed. The measured signal is based on the residence time of the tagged nucleotide rather than from the tagged end of a terminal incorporation. You can also have problems with pulses merging...
Forum: Introductions 11-29-2012, 11:02 AM
Replies: 0
Views: 890
Posted By ELoomis
Hello from Davis, CA

Hi all,
My name is Erick Loomis and I'm a Genetics grad student at UC Davis. I'm a long time creeper and relatively new poster here. I'm a wet-lab molecular biologist by training, but I'm also a...
Forum: Bioinformatics 11-29-2012, 10:17 AM
Replies: 132
Views: 55,633
Posted By ELoomis
Thanks! I downloaded and installed v1.2 and get...

Thanks! I downloaded and installed v1.2 and get an error when I try --discard-untrimmed. It doesn't seem to recognize that option, but I do see "--untrimmed-output=FILE" which accomplishes the same...
Forum: Bioinformatics 11-28-2012, 11:09 AM
Replies: 132
Views: 55,633
Posted By ELoomis
Filtering out reads lacking adapters

I'm trying to use cutadapt to remove an adapter sequence from my reads but I'd also like to discard any sequences that do not have an adapter (the adapter was added in an enrichment step prior to...
Forum: Bioinformatics 09-27-2012, 12:13 PM
Replies: 648
Views: 192,860
Posted By ELoomis
Filtering out low poorly converted reads

I'm using the non-CpG context cytosines as a measure of conversion efficiency for my sample, and I'd like to filter out any reads with a particularly low efficiency. This might be a bigger problem...
Forum: General 09-14-2011, 11:06 AM
Replies: 11
Views: 2,854
Posted By ELoomis
I see. PacBio might not be able to answer the...

I see. PacBio might not be able to answer the proportion question. The RS currently uses a passive loading approach for the SMRTcell, so smaller molecules have a competitive advantage.
In other...
Forum: General 09-14-2011, 10:27 AM
Replies: 11
Views: 2,854
Posted By ELoomis
PacBio is the way to go for trinculeotide...

PacBio is the way to go for trinculeotide repeats. As mentioned already, other methodologies will be limited by short readlength even if they can get past problems resulting from PCR amplifying your...
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