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