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Forum: Sample Prep / Library Generation 12-12-2011, 07:06 PM
Replies: 73
Views: 41,300
Posted By angelawu
Hi! Not sure if this issue of gel vs...

Hi!

Not sure if this issue of gel vs bioanalyzer has been resolved yet, but I have some thoughts about this.

1) In your second uploaded pdf, the intensity on the bioanalyzer chip looks very...
Forum: Bioinformatics 06-14-2011, 11:22 AM
Replies: 36
Views: 18,108
Posted By angelawu
Oh, the adapter sequences are not identical. If...

Oh, the adapter sequences are not identical. If you look closely at the middle portion of the sequences, there is a barcode in the middle that is different for each sequence. But I also do not think...
Forum: Bioinformatics 06-14-2011, 10:47 AM
Replies: 36
Views: 18,108
Posted By angelawu
Hi earonesty, Thanks for getting back to...

Hi earonesty,

Thanks for getting back to me!
Here is an example of the output I received:

Scale used: 2.2
Threshold used: 101 out of 40000
Adapter TruSeq-Adapter1...
Forum: Bioinformatics 06-13-2011, 04:25 PM
Replies: 36
Views: 18,108
Posted By angelawu
Question about fastq-mcf

Hi,

I encountered an issue when using fastq-mcf on my GA2 generated 1x36 reads, and wondering if you could shed some light.

So I made my fasta file with all the TruSeq adapter sequences in...
Forum: Bioinformatics 05-02-2011, 08:32 PM
Replies: 0
Views: 1,427
Posted By angelawu
Using trimmed reads in bwa (PE100bp data)

Hi All,

Bioinformatics newbie here, so excuse me if I ask a dumb question (to which the answer could not be found in the bwa manual).

I generated paired-end 100bp reads from genomic DNA, and...
Forum: Epigenetics 10-08-2010, 12:46 PM
Replies: 5
Views: 3,460
Posted By angelawu
Basically the GC rich sequences will be...

Basically the GC rich sequences will be over-represented. It has been published here:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862719/
Forum: Sample Prep / Library Generation 10-08-2010, 11:51 AM
Replies: 1
Views: 2,406
Posted By angelawu
BUMP! I just posted this same question under the...

BUMP! I just posted this same question under the epigenetics forum!
Forum: Epigenetics 10-08-2010, 11:41 AM
Replies: 5
Views: 3,460
Posted By angelawu
WGA Amplification for ChIP samples prior to Seq?

Hi,

I am working with small cell number ChIP-seq, and was wondering if anyone has any experience doing a WGA or similar after the ChIP step, before going on to make the library and seq?

I...
Forum: Bioinformatics 08-10-2010, 03:43 PM
Replies: 2
Views: 1,540
Posted By angelawu
Oh, and one additional thing - it works fine if I...

Oh, and one additional thing - it works fine if I do a 1-sample analysis...
Forum: Bioinformatics 08-10-2010, 03:40 PM
Replies: 2
Views: 1,540
Posted By angelawu
I also get weird outputs...

Hi,

I'm going to help bump up your post because I am also getting weird outputs from cisGenome. My bioinfo skills are negative, so please bear with any idiotic comments I might make...

I also...
Forum: Helicos / Direct Genomics 02-19-2010, 11:50 AM
Replies: 1
Views: 5,726
Posted By angelawu
I currently use Helicos for my low quantity...

I currently use Helicos for my low quantity samples (picogram level) and it is working far better than Illumina. The reason is because the tSMS allows you to get individual reads, whereas for...
Forum: Sample Prep / Library Generation 02-19-2010, 11:41 AM
Replies: 10
Views: 8,325
Posted By angelawu
With regard to the large mate pair libraries, you...

With regard to the large mate pair libraries, you might find this page helpful, particularly in the "More on Fragmentation" section.
...
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