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Forum: Sample Prep / Library Generation 02-12-2016, 01:07 AM
Replies: 289
Views: 169,004
Posted By adamreid
Problems with low input single-cell RNA-seq

We are trying to sequence RNA from individual small cells.

We are sorting by FACS and using SmartSeq2 and Nextera XT to make libraries.

We have had several problems.

We get rRNA...
Forum: Sample Prep / Library Generation 02-12-2016, 12:16 AM
Replies: 1
Views: 1,618
Posted By adamreid
Problems with low input single-cell RNA-seq

We are trying to sequence RNA from individual small cells.

We are sorting by FACS and using SmartSeq2 and Nextera XT to make libraries.

We have had several problems.

We get rRNA...
Forum: Literature Watch 09-21-2010, 01:57 AM
Replies: 46
Views: 44,021
Posted By adamreid
Detecting alignment collapse

Hi,

I want to check my genome sequence for collapsed, tandemly repeated genes. It seems to me that I could use software for detecting CNVs in that I am looking for significantly increased read...
Forum: RNA Sequencing 01-08-2010, 04:07 AM
Replies: 18
Views: 17,678
Posted By adamreid
Hi Xi, It is often the case that RNA levels...

Hi Xi,

It is often the case that RNA levels do not relate to protein levels. There are various different ways in which cells control the translation rate of mRNA into protein. These include mRNA...
Forum: RNA Sequencing 11-17-2009, 06:24 AM
Replies: 155
Views: 68,945
Posted By adamreid
Hi Xi, I guess I'm asking whether there...

Hi Xi,

I guess I'm asking whether there is/ought to be a correction for gene length because more reads are expected to map to longer genes.

Something else I was wondering about was the use of...
Forum: RNA Sequencing 11-16-2009, 07:46 AM
Replies: 155
Views: 68,945
Posted By adamreid
Hi there, When using DEGexp with read counts...

Hi there,

When using DEGexp with read counts for each gene, how are the read counts normalised? I've put dummy values in for gene lengths. Does it use these, expecting
no exons?

Adam
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