Hi, I am using the genome browser to view BAM files which have been trimmed to remove overlapping read ends for Illumina PE reads. It appears the browser is not correctly placing the clipped reads, see the example below. The browser removes the clipped part of the read, but the remaining part is always positioned at the start of the alignment, meaning that reads on the reverse strand will be misplaced. Is this a bug or am I doing something wrong?
Cheers, Ola Read name: HWI-ST344_0091:6:1204:11502:145261#CTTGTA Position: chr1:31021473-31021509 Band: 1p35.2 Genomic Size: 37 Alignment Quality: 60 CIGAR string: 63S37M (63 Skipped, 37 (mis)Match) Tags: AM:37 LB:cw19 MD:100 NM:0 RG:H3k27ac SM:37 XT:U X0:1 X1:0 XM:0 XO:0 XG:0 Flags: 0x93: (0x80) Read 2 of pair | (0x10) Read is on '-' strand | (0x03) Properly paired Note: although the read was mapped to the reverse strand of the genome, the sequence and CIGAR in BAM are relative to the forward strand. Alignment of HWI-ST344_0091:6:1204:11502:145261#CTTGTA to chr1:31021473-31021509: 00000064 GGAGGCTGAGGCACGAGAATCAATTGAACCTGGGAGG 00000100 >>>>>>>> | | || |||| | | | || >>>>>>>> 31021473 atctctactaaaaatacaaaaaattagccaggcgtgg 31021509 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
