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Code Block
titleSCP the data over
Get a couple of .bam and .bai files (for a given sample, you'll need both .bam and .bai files) from the hisat mapping results here:
 /corral-repl/utexas/BioITeam/Within your scratch directory, under my_rnaseq_course_2016/day_3_partA/gene_counting_exercise/hisat_results/

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crc

KdelR

Nacalpha

CG8979

CG4389

Vha68-2

regucalcin

CG3835

CG1746


Just type the gene name into the text box to look for the gene. Notice you'll need to zoom in and out to see the whole gene. See if you can identify spliced alignments. Look to see how coverage is at exons compared to introns. 


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