Hello,
when I align paired end fastq reads mapping to two different chromosomes using BWA, I typically get this result:
ILLUMINA-8B7A89:1:33:5159:13399#TAGCTTA#0 65 chr22 21854387 37 30M chr9 132720172 0 TGGCCCAACGATGGCGAGGGCGCCTTCCAT
GEFGGGEBEEEEEEEEEAEECDC==BCCBA
ILLUMINA-8B7A89:1:33:5159:13399#TAGCTTA#0 129 chr9 132720172 37 30M chr22 21854387 0 TCTGCTGAGCAGCGGGATCAATGGCAGCTT
FBFDEAEGEGGGEGGGDF5GGGGGGGGBGD
where BWA correctly reports the alignment and labels the read as 'not mapped in proper pair' (flag 2 off).
When I try the same using Bowtie I get a completely different result, with the paired read flagged as unmapped:
ILLUMINA-8B7A89:1:33:5159:13399#TAGCTTA#0 77 * 0 0 * * 0 0 TGGCCCAACGATGGCGAGGGCGCCTTCCAT GEFGGGEBEEEEEEEEEAEECDC==BCCBA
ILLUMINA-8B7A89:1:33:5159:13399#TAGCTTA#0 141 * 0 0 * * 0 0 TCTGCTGAGCAGCGGGATCAATGGCAGCTT
FBFDEAEGEGGGEGGGDF5GGGGGGGGBGD
Notably, when I map the two fastq as single reads, Bowtie reports the correct mapping to Chr9 and 22. I tried to play with Bowtie parameters with no luck. Of course I could try to output the 'unmapped' reads and remap as single reads but this is more complex and highly inefficient. Is there any Bowtie setting that allows me to correctly map 'flag-2-off' reads?
Thank you in advance,
Rocco
when I align paired end fastq reads mapping to two different chromosomes using BWA, I typically get this result:
ILLUMINA-8B7A89:1:33:5159:13399#TAGCTTA#0 65 chr22 21854387 37 30M chr9 132720172 0 TGGCCCAACGATGGCGAGGGCGCCTTCCAT
GEFGGGEBEEEEEEEEEAEECDC==BCCBA
ILLUMINA-8B7A89:1:33:5159:13399#TAGCTTA#0 129 chr9 132720172 37 30M chr22 21854387 0 TCTGCTGAGCAGCGGGATCAATGGCAGCTT
FBFDEAEGEGGGEGGGDF5GGGGGGGGBGD
where BWA correctly reports the alignment and labels the read as 'not mapped in proper pair' (flag 2 off).
When I try the same using Bowtie I get a completely different result, with the paired read flagged as unmapped:
ILLUMINA-8B7A89:1:33:5159:13399#TAGCTTA#0 77 * 0 0 * * 0 0 TGGCCCAACGATGGCGAGGGCGCCTTCCAT GEFGGGEBEEEEEEEEEAEECDC==BCCBA
ILLUMINA-8B7A89:1:33:5159:13399#TAGCTTA#0 141 * 0 0 * * 0 0 TCTGCTGAGCAGCGGGATCAATGGCAGCTT
FBFDEAEGEGGGEGGGDF5GGGGGGGGBGD
Notably, when I map the two fastq as single reads, Bowtie reports the correct mapping to Chr9 and 22. I tried to play with Bowtie parameters with no luck. Of course I could try to output the 'unmapped' reads and remap as single reads but this is more complex and highly inefficient. Is there any Bowtie setting that allows me to correctly map 'flag-2-off' reads?
Thank you in advance,
Rocco
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