why my transcript doesnt had the pvalue adj or fold change

deseq2

#1

i used Star and featureCounts and after that Deseq2 then download the data and put it on the exel to find my transcript which was the PER3…
( ENST00000377532.7) this is my transcript number. but it doesnt had the data i need like P value or fold changes,
why this happend ?
its because my workflow or the data im using ?


#2

Are these values in the original tabular file downloaded from Galaxy?

If yes, then the problem is with Excel. There is likely some formatting conflict causing the import or display of those columns to fail.


#3

so if i dont get my data to galaxy, is there any way to search to whole data for one transcript id ? its not working with Ctrl+F.


#4

i found the transcript but its still doesnt had any values
like you see in the file i send,


#5

The line is empty because no reads had coverage over that transcript region after being processed by DESeq2.

To search an entire file with a keyword or regular expression, try the tool Select.

Terms like this will work for a query like yours: “ENST00000377532.7” in the first column of data

Use the matching “Matching” option with one of these.

Less specific:

ENST00000377532

More specific:

ENST00000377532\.7

Very specific:

^ENST00000377532\.7

You could find or remove all lines like this with the tool Filter data on any column using simple expressions.

Find (isolate) all lines with no counts:

c2==0

Remove all lines with no counts:

c2!=0

#6

so if i do this with limma or edgeR maybe i get values for this transcript ?


#7

You can try that. Adjusting the settings for DESeq2 might also help. It depends on a few factors, including the content of the original count files and how these tools compute coverage/fold changes.

Be aware this could be a legitimate result no matter what different tool settings you use. See the tool manuals and support forum at http://bioconductor.org/ to learn more about settings and functions for these tools.


#8

does the galaxy have any tool for time-course rna seq analysis . and if it doesnt, how can i suggest one? whats the process to use a new tool in galaxy ?


#9

Limma, EdgeR, and DEseq2 can all handle time series analysis. Build this into your factor/factor-levels/contrasts. There isn’t a specific tutorial that covers this, but each tool form explains how to set-up an experimental design with link-outs to more resources.

I think you already have the GTN Tutorials link. Many new tutorials were recently published. And this unpublished tutorial covers more: https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html. Feedback for all tutorials is welcomed via the form at the bottom of the “hands-on” module.

Nearly any tool can be wrapped for Galaxy if you had something else in mind. Check the ToolShed first to see if it already exists. Not all tools are hosted on public servers. You can wrap tools yourself or ask the IUC if there are any plans/suggest a new tool.