Question: Depth Command In Sam Tools
0
Els Willems • 30 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
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modified 5.7 years ago
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Jennifer Hillman Jackson ♦ 25k
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written
5.7 years ago by
Els Willems • 30
