I used BWA to map 454 reads and the outputs were in SAM format.The sixth column is CIGAR which shows matching(M)/insertion(I)/deletion(D).However,there are another two operations which I don't understand their meanings:
What do Soft clip and Hard clip mean?Do they clip reads before mapping? and what's the difference between them?
For example,I get one CIGAR as:
4S20M1D20M15S
how to explain 4S and 15S?
Thank you!
S Soft clip on the read (clipped sequence present in <seq>)
H Hard clip on the read (clipped sequence NOT present in <seq>)
For example,I get one CIGAR as:
4S20M1D20M15S
how to explain 4S and 15S?
Thank you!
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