Hello Dikla,

Information in the sixth field of these same files will provide information about why the calculations for individual genes/transcripts were not performed. Possible values are explained in the tool documentation:
http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff

This particular region appears to have low coverage compared to the surrounding regions (e.g. low abundance), but this is of course only a small sample, and it is difficult to know about other criteria considered by the tool from the graphic (proper pairing, multiple map locations, etc.).

But if you believe that higher abundance transcripts are preventing lower abundance transcripts from being evaluated, or even just suspect that and want to test, you could try running Cufflinks with the option "Perform quartile normalization: Yes". Using "Perform Bias Correction: Yes" is also another parameter to explore (requires a reference genome).

The Cufflinks web site is a great resource to learn more about these parameters and the Galaxy tool form has each included as an option.

Hopefully this helps,

Jen
Galaxy team


On 2/14/13 1:48 AM, Dikla Aharonovich wrote:
Hello,

We are using BAM to map Illumina reads to a bacterial genome, followed
by Cufflinks o get the FPKMs.  We have come across many genes for which
we get FPKM=0 (using both gene and transcript expression) even though
there are reads mapping to these gene IDs (e.g. the region between the
dashed lines in the attached screenshot).  Can anyone suggest a
reason/fix for this?

Thanks

Dikla



___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/


--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to