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CGATOxford / cgat

Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps
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gtf2table swapping spliced and unspliced reads #20

Closed IanSudbery closed 10 years ago

IanSudbery commented 10 years ago

Running gtf2table with gtf2table.py -b bamfile.bam -c read-counts -L /dev/null --library-type firststrand

is producing output where the number of outputed as counted_splice is the number of unspliced reads and counted_unspliced is the number of spliced reads.

AndreasHeger commented 10 years ago

Hi Ian,

do you have an example data file?

Best wishes, Andreas

IanSudbery commented 10 years ago

Hi Andreas,

You can see this with /ifs/projects/proj028/iCLIP_pilot_paired/test.gtf and /ifs/projects/proj028/iCLIP_pilot_paired/test.bam

Ian

AndreasHeger commented 10 years ago

Thanks, indeed that was a simple swap. Fixed!

Apologies for the delay in fixing.