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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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READ_LENGTH #36

Closed e-manduchi closed 9 years ago

e-manduchi commented 9 years ago

The template.cfg file now has a READ_LENGHT field. Does this mean that PORT won't work if different samples in the study have different read lengths?

eunjijunekim commented 9 years ago

I would suggest equalizing the read lengths before running PORT.

However, PORT will work even if different samples have different read lengths. READ_LENGTH is a parameter used in get_master_list_of_intergenic_regions.pl and having different read lengths won't have a huge impact on the results. If you choose to use samples with varying read lengths, you can use the max read length in the config file.