Lu Yang

5 Questions 7 Answers 0 Followers

Questions related from Lu Yang

What ratio of AMPure beads/sample should I use to remove short primer dimers but keep as many my 3kb fragments as possible?

Assuming that the PCR condition is optimal, but I still get primer dimers that I have to get rid of for downstream experiments, what ratio should I use to keep my fragments as much as...

29 August 2017 172 4 View

How can I convert a .gff file to a .gff3 or .gtf file, which could be detected by Cufflink Galaxy?

I'm using cufflink on Galaxy. It only uses gff3 or gtf. I feel there are no differences among gff3, gff2 and gff. The attribute part differs a little bit but does that really matter? Also I used...

28 August 2015 4,699 12 View

Why is there only one peak at 18S, but almost no 28S in the bioanalyzer results?

I did a nano RNA chip to check the RNA integrity. All eight samples have a clear peak at 18S, but almost none at 28S. What does this mean? If they are degraded, there should be no obvious peak at...

28 August 2015 7,886 5 View

For a reference for RNAseq analysis, should I merge my own transcriptome assemblies or use a published genome from a near species?

I want to do a RNAseq analysis of Papilio.glaucus and now we have the sequences from 12 samples. I need a reference if I want to use Cufflinks/Tophat2. Should I merge my own transcriptome...

18 August 2015 4,223 5 View

How can I pull the longest isoform out of an assembly in Trinity?

Is there any existing script to do that?

28 April 2015 9,229 4 View