I am currently extracting unaligned reads with the syntax below:-
According to http://picard.sourceforge.net/explain-flags.html, unmapped reads are flagged as 77 or 141.
These are some of the reads that I've extracted
From the XT:AU and XT:AR tags, does this mean that these reads are aligned at unique or at repeated regions? Or are they really unaligned reads? I was under the impression that for unaligned reads, there will be a "*" at the reference column.
Thanks
Regards,
Joanne
Code:
samtools view -f 4 *.bam
These are some of the reads that I've extracted
HTML Code:
HWI-ST715:180:D0JHKACXX:4:2307:5231:174176 93 4340.m000924 1187 23 76M = 1187 0 CGATGGCGCCCAAGGCCGAGAAGAAGCCCGCGGAGAAGAAGCCGGCCTCCGATAAA CCGGCGGAGGAGAAGGAGAA <DBBB;@BDCCDBDDDBDDDDDDDDDDDCEDEEECHHGJIIIJJIIIJJJJJJJJHJJJJJJJHHHHHFFFFFCCC XT:A:U NM:i:1 SM:i:23 AM:i:0 X0:i:1 X1:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:0A75 XA:Z:4340.m000879,-671,76M,2; HWI-ST715:180:D0JHKACXX:4:1307:20018:59034 77 4340.m000900 388 0 76M = 388 0 GTTCTCCCCGGCGAACTCGCGAAGCACGCCGTCTCCGAGGGCACTAAGGCTGTTAC CAAGTTCACAAGTTCTTGAT CCCFFFFFHHHHHJJJJJJJJJJJJJJIHHFFDDEEDBDDDDBDCDDDDDDDDDDDDDDDDDDEDDCDCDEEDDDA XT:A:R NM:i:1 SM:i:0 AM:i:0 X0:i:2 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:75A0 XA:Z:4340.m000899,+388,76M,1; HWI-ST715:180:D0JHKACXX:4:1206:2590:114359 77 4340.m000900 391 0 76M = 391 0 CTCCCCGGCGAACTCGCGAAGCACGCCGTCTCCGAGGGCACTAAGGCTGTTACCAA GTTCACAAGTTCTTGATCCG CCCFFFFFHHHHHJJJJJJJJIJIIIJHEFEEEDBDDDDDDDDDDDDDDDDDDDCDDCDEEDDDDCCDECDDDDDA XT:A:R NM:i:4 SM:i:0 AM:i:0 X0:i:2 X1:i:0 XM:i:4 XO:i:0 XG:i:0 MD:Z:72A0T0G0A0 XA:Z:4340.m000899,+391,76M,4;
Thanks
Regards,
Joanne
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