I get this error when running picard ValidateSamFile in a RNA-Seq bam file produced by hisat2:
ERROR: Record 52, Read name K00103:277:HL7HMBBXX:6:2109:23551:26054, Mate negative strand flag does not match read negative strand flag of mate
This is the read in the bam file:
samtools view -@ 12 hisat2_sort.bam | grep "K00103:277:HL7HMBBXX:6:2109:23551:26054"
K00103:277:HL7HMBBXX:6:2109:23551:26054 69 1 3747256 0 * = 3747256 0 CTGGCTACACAAACAGGACCCAACATTCTGCTGCTTACAGGAAACCCATCTCAGGGAAAAAGACAGACACTACCT AAFFFJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJFJJFJJJJJJJJJJJJJJJFJJJJJJJJ YT:Z:UP RG:Z:F72_tumor_R1 K00103:277:HL7HMBBXX:6:2109:23551:26054 153 1 3747256 60 75M = 3747256 0 ATTGACCATATAATTGGTCACAAAATAGGCCTCAACAGAAACAAAAATATTGAAATTGTCCCATGTATCCTATCA JFJFJJJAFJJ<JFA7F<F<F<FJ-<AAA<-<7FJ<A-J-J<JJJF<FJFJJJJJJJJJJJJJJJJJJJFFFFA< AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:75 YT:Z:UP NH:i:1 RG:Z:F72_tumor_R1
I don't know what's going on and I need to fix this.
Any help would be appreciated.