Alignment of RNA-seq reads to reference genome: GMAP

You should be able to answer these questions if you successfully completed the section: Align the experimental transcripts to the reference genome .

Questions

• 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

Compare the transcripts to the reference transcriptome

You should be able to answer these questions if you successfully completed the section: Compare the experimental transcripts to the reference annotation .

Questions

• What do the output files represent? Hint
• How many putative new isoforms do we have in out dataset as compare to the reference? Hint

Next

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