Transcriptome assessment: Checkpoint

Section: Transcriptome assessment [4/4].

• What is the advantage of indexing the reference genome before running the alignment?
• What is the difference between a splice-aware and a splice-unaware mapper? What is the advantage of the first?
• How is the GFF3 format outputted by GMAP different from a standard GFF/GTF? Hint
• How would you change the command line to get standard SAM output? Hint
• What more information could you get from the SAM output? Hint
• Repeat the alignment step outputting SAM fomat. How many reads are mapped? Comment on the CIGAR strings. Hint
• What do Cuffcompare output files represent? Hint
• How many putative new isoforms do we have in out dataset as compare to the reference? Hint

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We are mostly done! Questions welcome :)

• Acknowledgements

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