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Let's parse the bam file to pull out just spliced alignments.

Looking at the CIGAR string at the CIGAR string

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Answer

Code Block

title	Looking

for spliced alignments

 samtools view accepted_hits.bam | cut -f 1,6 | grep 'N'|head

The

The CIGAR string "66M76N9M" represents a spliced sequence. The codes mean:

66M - the first 66 bases match the reference
76N - there are then 76 bases on the reference with no corresponding bases in the sequence (an intron)
9M - the last 17 bases match the reference

Exercise 2b: What is the read ID for one of these reads with spliced alignment?

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