Cufflinks problem sorting

[RNAddict]

I have mapped reads to a reference using tophat/bowtie. I then use the output from tophat with cufflinks... and I get the following error "sort order of reads in BAMs must be the same."

I have tried sorting my tophat output with samtools... but that still doesn't work.

I am confused because I am only using 1 BAM file... so I do not understand what it is comparing my BAM file to that it thinks the sort orders are different.

Anyone know about this? I have seen the error posted in different threads but those are dealing with cuffmerge or cuffdiff which would be joining or comparing multiple BAM files.

[vyellapa]

Use picards ReorderSam.jar if you believe sort order is the issue.

[RNAddict]

Below is an example from my accepted_hits.bam file I am trying to run with cufflinks

HWI-1KL118:19:C099JACXX:8:2303:8200:82055	99	comp10000_c1_seq1	29	3	48M1D52M	=	88	159	ATCTTACCCTGTCCCCACTCTCTAAGAAGAAGAGCTATTTTTCTATGCTGCAAAATATTTCAATATTAATCAGGAAAAAAACAGGAACAGAACAAAAACA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:1	NH:i:2	CC:Z:comp9978_c0_seq1	CP:i:1751	HI:i:0
HWI-1KL118:19:C099JACXX:8:1104:11427:111619	419	comp10000_c1_seq1	31	3	100M	=	64	133	CTTACCCTGTCCCCACTCTCTAAGAAGAAGAGCTATTTTTCTATGCTTGCAAAATATTTCAATATTAATCAGGAAAAAAACAGGAACAGAACAAAAACAA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:2	CC:Z:comp9978_c0_seq1	CP:i:1750	HI:i:0
HWI-1KL118:19:C099JACXX:8:2204:11486:188570	99	comp10000_c1_seq1	31	3	100M	=	64	133	CTTNCCCTGTCCCCACTCTCTAAGAAGAAGAGCTATTTTTCTATGCTTGCAAAATATTTCAATATTAATCAGGAAAAAAACAGGAACAGAACAAAAACAA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:1	NH:i:2	CC:Z:comp9978_c0_seq1	CP:i:1750	HI:i:0
HWI-1KL118:19:C099JACXX:8:2308:14574:10360	419	comp10000_c1_seq1	36	3	100M	=	104	168	CCTGTCCCCACTCTCTAAGAAGAAGAGCTATTTTTCTATGCTTGCAAAATATTTCAATATTAATCAGGAAAAAAACAGGAACAGAACAAAAACAAAACAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:2	CC:Z:comp9978_c0_seq1	CP:i:1745	HI:i:0
HWI-1KL118:19:C099JACXX:8:2105:2435:109977	355	comp10000_c1_seq1	43	3	100M	=	52	109	CCACTCTCTAAGAAGAAGAGCTATTTTTCTATGCTTGCAAAATATTTCAATATTAATCAGGAAAAAAACAGGAACAGAACAAAAACAAAACACAATAGAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:2	CC:Z:comp9978_c0_seq1	CP:i:1738	HI:i:0
HWI-1KL118:19:C099JACXX:8:2302:5607:56272	137	comp10000_c1_seq1	43	3	100M	*	0	0	CCACTCTCTAAGAAGAAGAGCTATTTTTCTATGCTTGCAAAATATTTCAATATTAATCAGGAAAAAAACAGGAACAGAACAAAAACAAAACACAATAGAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:2	CC:Z:comp9978_c0_seq1	CP:i:1738	HI:i:0
HWI-1KL118:19:C099JACXX:8:2307:6056:194919	99	comp10000_c1_seq1	43	3	100M	=	64	121	CCACTCTCTAAGAAGAAGAGCTATTTTTCTATGCTTGCAAAATATTTCAATATTAATCAGGAAAAAAACAGGAACAGAACAAAAACAAAACACAATAGAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:2	CC:Z:comp9978_c0_seq1	CP:i:1738	HI:i:0

Does anyone know if there are multiple reference sequences with the exact same name if that would cause this error?

EDIT: I found the problem... it was that I had multiple reference sequences with the same name. Removing the duplicates got rid of the error.