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Forum: Metagenomics 06-23-2017, 02:04 AM
Replies: 3
Views: 4,472
Posted By KateShepard
16S sequencing tissue - host DNA contamination

Dear all,

We are planning to use human/mouse intestinal tissues/biopsies for V4 microbiome sequencing. I am worried that the large amount of host DNA from the tissue will result in amplification...
Forum: RNA Sequencing 05-19-2016, 03:18 AM
Replies: 0
Views: 2,115
Posted By KateShepard
how does cuffdiff calculate replicate FPKM values?


I have two conditions, 5 replicates for each. After running cuffdiff I noticed the FPKM values in gene_exp.diff for one condition do not make sense.

For example, the 5 replicate FPKM...
Forum: RNA Sequencing 04-28-2016, 07:52 AM
Replies: 3
Views: 3,338
Posted By KateShepard
CummeRbund for one condition (multiple biological replicates)

Thank you for your replies.

CummeRbund looks extremely useful, however I am having trouble working out how to use Cufflink data which originates from one condition only (multiple biological...
Forum: RNA Sequencing 04-25-2016, 08:18 AM
Replies: 3
Views: 3,338
Posted By KateShepard
biological replicates cuffmerge?

Dear forum,

I have 5 RNA-seq biological replicates and wish to examine the expression levels of specific genes/pathways of interest (high/low/not expressed) (no differential expression analysis)....
Forum: RNA Sequencing 04-15-2016, 07:37 AM
Replies: 1
Views: 3,157
Posted By KateShepard
cross species RNA-seq/orthologs

Dear Forum,

I am completely new to RNA-seq analysis so would be very appreciative of any advice regarding my query.

I have multiple RNA-seq samples from two closely related species, and would...
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