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Forum: Illumina/Solexa 08-26-2013, 03:04 PM
Replies: 0
Views: 2,434
Posted By days369
Question High proportion of PolyT reads

Hi everyone,

I recently sequenced several cDNA libraries on HiSeq platform. But all the libraries ended up with more than 50% of polyT reads and not a lot of polyA reads. This phenomena made me...
Forum: Sample Prep / Library Generation 04-10-2013, 02:39 PM
Replies: 1
Views: 1,985
Posted By days369
Can I store fragmented DNA in freezer for a while?

Hi all,

I am a newbie for sequencing library construction. Before I start to fragment my DNA samples, I am wondering whether I can store the fragmented DNA in freezer before I continue the end...
Forum: RNA Sequencing 04-05-2011, 02:42 PM
Replies: 2
Views: 5,460
Posted By days369
Can anybody kindly address some of the questions?...

Can anybody kindly address some of the questions? My post has been ignored :(
Forum: RNA Sequencing 03-30-2011, 12:21 AM
Replies: 2
Views: 5,460
Posted By days369
RNA-Seq Quantification and Differential Expression Analysis

I am currently analyzing RNA-Seq data from bacterial transcriptome. Here I have several questions regarding gene expression quantification and differential expression analysis.

1. For Partially...
Forum: Bioinformatics 08-16-2010, 02:29 PM
Replies: 4
Views: 2,784
Posted By days369
Hi mrawlins, THanks for answering. Do you...

Hi mrawlins,

THanks for answering. Do you have any idea about the common quality score people use to trim sequences?
Forum: Bioinformatics 08-16-2010, 01:29 PM
Replies: 4
Views: 2,784
Posted By days369
Do I need to trim the sequences like this?

When I checked my solexa sequencing reads, i found that some of them are like this.


NNNNNNNNAGGNNNNNGGAGNGNNGNNNCAGNGNTGNNNNNNNNNNNNNANNNNNNGNNNNNNNTGGNGGNNNNNNNN
+...
Forum: Bioinformatics 08-06-2010, 10:51 PM
Replies: 5
Views: 12,869
Posted By days369
kmcarr, thanks so much. your reply is really...

kmcarr, thanks so much. your reply is really helpful.

I guess that my reads should be produced using the Illumina paired end protocol, so most of them are in --fr orientation.

But a small...
Forum: Bioinformatics 08-06-2010, 01:36 PM
Replies: 5
Views: 12,869
Posted By days369
Bowtie Paired-end options

Hi everyone,

I just began to use bowtie to map my solexa paired-end reads to a genome. I found that bowtie has three options to specify the orientation of the paired-end reads, --fr, --rf, and...
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