DE Analysis (known miRNA)

[Former user]

hi Edu!

I run the DE Analysis for known miRNA but the samples are not correctly assigned within the treatment classes (although I have prepared target.txt file just according the example in manual). For example on density plots of the distribution of the counts in PDF report, the different replicates shall be represented with the same colour. in my case everything is mixed. how I can be sure that samples were correctly assigned with their treatments and the contrast groups compared accurately?

[Eduardo Andres Leon]

Hi Anonymous! ;)

Files are sorted taking into account the columns names in your tab file and your Filename column in the targets. Could you include your target.txt and ini file to check one thing ? Thanks in advance

[K.M. Kwiatkowska]

ok. thanks for your answer! & pardon the 'anonymous' - I forgot to log in. please see the target.txt attached

cheers!

[K.M. Kwiatkowska]

Edu, btw, just to confirm: by the 'tab' file we understand the *ReadCount.tab file, correct? thanks!

[Eduardo Andres Leon]

jaja no problem ;)

I see a "strange" thing in you target.txt, if you order the targets.txt file according with the Filename column, Treatment/Names columns are mixed

So I recommend you to rename your fastqs: Sample_A_M_exp1_cut2_nat_bw1 -> A_exp1.fq Sample_A_M_exp2_cut2_nat_bw1 -> A_exp2.fq

....

It is important that Filenames, names and treatments contains a very similar name so the "sorting step" don't mix samples. The other possible option is to change the Name and treatment values in your target.

[Eduardo Andres Leon]

Edu, btw, just to confirm: by the 'tab' file we understand the ReadCount.tab file, correct? thanks!*

Yes!

[K.M. Kwiatkowska]

howdy Edu! I changed the names so the files are sorting properly (as you can see on print screen of terminal) but the mess on density plot of the distribution of the counts continue as it was ... any clues? best!

[K.M. Kwiatkowska]

ok. solved. thanks Edu

[Eduardo Andres Leon]

???? It seems that my answer (9th March 18:58) did not arrived here (I answered you by mail)

What did you change? Regards

[K.M. Kwiatkowska]

I changed the order of samples in target.txt file to exactly the same as column names in ReadCount.tab. (doesn't seem that it shall be the issue, but it worked) thanks, kat

[Eduardo Andres Leon]

The user changed the order of samples in target.txt file to exactly the same as column names in ReadCount.tab