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I'm trying to calculate depth of coverage for entire contigs for multiple samples. I have ran the following command:
java -Xmx2g -jar GenomeAnalysisTK.jar \
-R Ecoli/Ecoli.allSubTypes.fasta \
-T DepthOfCoverage \
-o ../Ecoli/all.tmpOut \
-I Ecoli/bamlist.list \
Where I've tried to generate a refSeq file with one line per contig.
I was expecting to have the output be in the form of a matrix with the various contigs as rows and the samples as columns.
Instead I got this looking file:
Locus Total_Depth Average_Depth_sample Depth_for_sample1
gi|312944605|gb|CP001855.1|:1 0 0.00 0
gi|312944605|gb|CP001855.1|:2 0 0.00 0
gi|312944605|gb|CP001855.1|:3 0 0.00 0
gi|312944605|gb|CP001855.1|:4 0 0.00 0
gi|312944605|gb|CP001855.1|:5 0 0.00 0
gi|312944605|gb|CP001855.1|:6 0 0.00 0
gi|312944605|gb|CP001855.1|:7 0 0.00 0
gi|312944605|gb|CP001855.1|:8 0 0.00 0
gi|312944605|gb|CP001855.1|:9 0 0.00 0
were each base is a row. right?
What am I doing wrong?