quantity of each replicate / id conversion

Question: quantity of each replicate / id conversion

2.6 years ago by

United Kingdom

azadjali • 0 wrote:

Hi I need an information about the quantity of genes in each replicates how to do it

I am using two different types of mice WT and knock out, the samples for both types were taken at 5 different age groups and there are 3 replicates for each. my targets will be to get the differential expression which I think I know how to do it but I also would like to know the gene quantity of each replicate.

final results in cuffdiff does not show quantity of each replicates separately. it shows the genes quantity of the 3 combines replicates together in in two different types of mice.

can you give any suggestion please

Also how to convert the Galaxy gene id (TCONS- or XLOC_) into ensembl id

N.B. my samples are RNAseq (paired-end)

regards Abdul

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modified 2.6 years ago • written 2.6 years ago by azadjali • 0

2.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The output of Cufflinks would show the gene count per replicate (per run). Maybe this will suit your needs?

To add in gene IDs (the ones you show are defaults by the tool), try using a reference annotation dataset from the source you wish to label these as. iGenomes is a good choice: http://support.illumina.com/sequencing/sequencing_software/igenome.html

There are other ways to try to annotate after the fact, but none are very satisfactory when based on common overlapping regions.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

2.6 years ago by

azadjali • 0

United Kingdom

azadjali • 0 wrote:

Thank you dear Jennifer

I think as you said the output of Cufflinks [appears in history as a file of: gene expression under the column of FPKM] but is there any way to read the raw counts of those genes instead of FPKM.

and thank you for the site iGenomes: http://support.illumina.com/sequencing/sequencing_software/igenome.html I will choose the ensembl reference annotation from it, hopefully it is in gtf. format.

I want to ask you for the mouse genome, will it be better to choose the genome from Galaxy or from other sources

actually soon I am going to send my samples for RNA sequencing and my supervisor wants me to do few things with the data (the output of galaxy- and prefer the ensembl IDs).

thank you again , appreciate your kind help

Abdul

ADD COMMENT • link written 2.6 years ago by azadjali • 0

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