Cigar after picard MergeBamAlignment
I got confused by the CIGAR in bam file. after MergeBamAlignment.
I have reads in uBam. Then it's converted into fastq and trimmed on 5' side. Then aligned with STAR and MergeBamAlignment the mapped Bam with the uBam to recover the tags.
Below is an example:
original fastq read
I did 5bp triming on the 5'side.
After STAR mapping.
K00206:101:HH7C2BBXX:1:1101:10003:10141 16 19 9113177 255 32M975N89M * 0 0 TGCCAACTGAGCAGCCTCCTCTACGGTCTTTCCTTGCTCTACATGGAAGAGGGCAAGTCTGGCCAGATTCACCTTCAGGATACTTTCCCCATGTCCTGTGGTTGAAACGGCTCCAAGGTTA JJJJJJJJJFJFAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ NH:i:1 HI:i:1 AS:i:120 nM:i:0 NM:i:0 MD:Z:121 jM:B:c,22 jI:B:i,9113209,9114183 XS:A:-
K00206:101:HH7C2BBXX:1:1101:10003:10141 16 19 9113177 255 5S32M975N89M * 0 0 TGCCAACTGAGCAGCCTCCTCTACGGTCTTTCCTTGCTCTACATGGAAGAGGGCAAGTCTGGCCAGATTCACCTTCAGGATACTTTCCCCATGTCCTGTGGTTGAAACGGCTCCAAGGTTATTATC JJJJJJJJJFJFAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA MD:Z:0T0G0C0C1A1T1A0G0C0A0G0C2C1T0C1A0C0G0G0T3T1C0T1G1T0C0T0A0C1T0G1A0A0G1G1G1A0A1T1T1G0C0C0A0G0A0T1C0A0C0C0T0T0C1G0G0A1A1T0T0T0C0C0C1A3C0C1G0T0G0G0T0T1A0A0A1G0G0C0T0C0C0A1G0G0T1A0 PG:Z:STAR RG:Z:E11_m_Mut-6-2_A2B5 NH:i:1 NM:i:87 UQ:i:3524 AS:i:120
It's aligned to the reverse strand. The SEQ in bam is fine. But the CIGAR has "5S" on the left. Is it supposed to be on the right? When I visualise the bam after MergeBamAlignment, it's full of mismatches because of the CIGAR.