Silvia Cereghini
Attachments2:07 PM (1 hour ago)

to me 
Dear Martin

I compared the diff expressed genes found by tuxedo and those by you MetaseqR analysis and I found that there are many differences and in either Fasteris or your analysis there are genes lost that we know are down regulated such as Ihh (in your case) , kcnj16 in Fasteris




I send you the Venny done on down regulated genes from -0.5 up. Could you explain me which filtering parameters were applied either by Tuxedo or by you, because the results should be the same

Thanks and sorry for disturbing you

silvia

#@
Silvia Cereghini
Jul 14 (3 days ago)

to me 
Dear Martin

Yesterday I sent the fastaq raw data obtained from Fasteris:  WT are GZS_17 -35, Mutant Heterozygous : GZS_34-36

In each case each sample correspond to pools of 2 embryos. So it could be performed the metadata analysis as you have already done for the other samples

But before we need to clarify the aspect of Filtering : I would like
to know how this is applied and which are the cut off values you use,
in other words as I asked previously if the values of for instance are
very low only in mutants do you exclude them?

On the other side, we must take in account that the mutant are
heterozygous mutants so we do not expect drastic decreases of
expression for that reason the cut off value instead -1 it would
preferably -0.75 , because this include many targets of Hnf1b that are
in fact downregulated.

Finally I was checking all the mails sent by Pantelis that I found in
an old computer because my computer was over las year and I found the
metadata analysis of E14.5 samples sent separately that are clearly
indicated in the input. The mistake arrived when all the links were
sent together.

I imagine you had this. If you want I can send back.

Once clarified the problem of filtering or not , the metadata analysis from all samples is done.

I am still trying to find a computer to convert the bam files to another that I could convert. For instance I could not open tha fastaq sent by Fasteris for that reason I did not have.

All the best

`Silvia
.
PS: as I mentioned in a previous mail we have applied  Toppfun to define GO terms , expression patterns disease etc. We would like rather with all these data to do gene regulatory networks (I saw papers that use i-Regulom based on Cytospace .Do you know these sofwares?