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itmat / Normalization

RNA-Seq normalization and quantification pipeline
https://github.com/itmat/normalization/wiki
GNU General Public License v3.0
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runall_quantify_exons working for single end data? #7

Closed e-manduchi closed 10 years ago

e-manduchi commented 10 years ago

Has this been fixed to work on single end data? Before github I had to modify the original script to run on single end data but adding -rpf to the call to quantify_exons.pl

eunjijunekim commented 10 years ago

this should work on single end data since we only keep the forward reads after the filter step.

e-manduchi commented 10 years ago

I know, but the reason I'm asking is that the original script I had got from Greg's home on the cluster would fail, even though only forward reads were kept, if one didn't give the -rpf option. This had to do with the code in within the else at line 202 (referring to the github line numbers). Basically I think the bit values which are checked in order to come up with true/false assignments for $forward_only, $reverse_only were assuming paired end data. So without the -rpf option one would enter that else clause and would end up with incorrect settings for these two variable. I had reported this to Greg who said I had to give the -rpf option and that worked.

eunjijunekim commented 10 years ago

Hi, I added '-se' option to runall_quantify_exons.pl script. When '-se' option is given, runall script will use -rpf option.

fossilfriend commented 10 years ago

Great timing! I gave it a try and ran into a couple of syntax errors:

syntax error at runall_quantify_exons.pl line 178, near "else" syntax error at runall_quantify_exons.pl line 204, near "}" Missing right curly or square bracket at runall_quantify_exons.pl line 205, at end of line Execution of runall_quantify_exons.pl aborted due to compilation errors.

eunjijunekim commented 10 years ago

sorry about that. please try again and let me know if you have any other problems.

fossilfriend commented 10 years ago

seems ok now! thanks