Dear all,

I am a Phd student working on chicken genomics, with limited experience in the 
bio-informatics field. I performed an RNA-Seq experiment with single end 50 bp 
reads to find differential gene expressions between different groups. I have 
mapped this data with Tophat and used flagstat and Picard to check the number 
of mapped reads.

To check the coverage of my genome, I could use the number of mapped reads and 
multiply this by the read length and divide by the genome size, but of course 
since I used mRNA as input material, average coverage will be low (only exons 
presents). I would like to use the Samtools Depth (as I read on SeqAnswers) to 
get the average coverage for a coveraged base AND the total base coverage, but 
this does not seem to be included in Galaxy. Does anyone know a way around 
this? Other useful tips and tricks are also welcomed. Thank you very much.

Have a nice day.

Yours Sincerely, Els

Ir. Els Willems
KU Leuven
Department of Biosystems
Division Livestock - Nutrition - Quality
Laboratory of Livestock Physiology
Kasteelpark Arenberg 30 bus 2456
B - 3001 Heverlee
T (+32) 016 32 17 29
F (+32) 016 32 19 94

The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at  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:

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

Reply via email to