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mapping file for RNASeq for human

mapping file for RNASeq for human
Answer
1/30/14 7:07 AM
Dear Sir,

I am working on data analysis for SOLiD sequencer generated data in which data is mapped against human hg19 genome and i did differentilal expression for the same and I want to show differential expression genes on pathway images. After reading the mapman manual i understood that mapman is exclusively for plant species.

Would you please let me know is it possible to generate mapping file for hg19 human genome ,if it is so can i give human genoem .fasta file directly in Mercator application for getting mapping file and against which sequence i need to blast my sequence.

Kindly let me know.


Thanks & Regards
Rehaman

RE: mapping file for RNASeq for human
Answer
1/30/14 10:16 AM as a reply to fazulur rehaman vempalli.
Dear Rehaman,

technically, you could do as you suggested and run the human transcriptome or proteome through the
mercator pipeline, but, since mercator computes functional annotation based on plant reference data only
the parts of the proteome that plants and human share would be reasonably annotated. And hence i would
strongly discourage using mercator for non-plant sequences.

best greetings,
Marc

RE: mapping file for RNASeq for human
Answer
1/30/14 12:03 PM as a reply to Marc Lohse.
Thanks for your quick reply Dr.Marc.

Regards
Rehaman