Hello Els,

Have you seen the tool "BEDTools -> Create a BedGraph of genome coverage"? This would give you the coverage numbers, then you could perform statistics on those numbers.


You could also "Convert from BAM to BED" (there is an option to split for spliced alignments) and if you had a bed file of transcripts, use tools in this group or tools in "Operate on Genomic Intervals" to generate statistics.

You could also create your own statistics using "Text Manipulation -> Compute" or "Join, Subtract and Group -> Group".

Hopefully one of these options works out for you.

Jen
Galaxy team


On 3/15/13 8:54 AM, Els Willems wrote:

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



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