Hi,
I am currently working on aligning paired-end short reads to a reference transcriptome. I am quite puzzled by the output which I am receiving from bowtie.
Currently the bowtie manual specifies that the 7th column of the output gives us the "number of other possible alignments that can be found on the reference as it was with the current alignment".
The following is a sample output from bowtie, i used the command -a to output all possible alignments (i am displaying only columns 1,3,7):
Please note this is paired-end alignment, so every two row represents the same alignment.
Look at the 7th column (3rd column in this case), the first line says we have 5 other similar alignments but there are only 4 other alignments from the same read and the last read says there is one other alignment, but where? Shouldn't bowtie print all other possible alignments with the -a command?
Does anyone know how to interpret this data?
Please help.
Thank you,
Kevin
I am currently working on aligning paired-end short reads to a reference transcriptome. I am quite puzzled by the output which I am receiving from bowtie.
Currently the bowtie manual specifies that the 7th column of the output gives us the "number of other possible alignments that can be found on the reference as it was with the current alignment".
The following is a sample output from bowtie, i used the command -a to output all possible alignments (i am displaying only columns 1,3,7):
HWUSI-EAS645:1:1:4:2033#0/2 | NM_001317 | 5
HWUSI-EAS645:1:1:4:2033#0/1 | NM_001317 | 5
HWUSI-EAS645:1:1:4:2033#0/2 | NM_022640 | 5
HWUSI-EAS645:1:1:4:2033#0/1 | NM_022640 | 5
HWUSI-EAS645:1:1:4:2033#0/2 | NM_020991 | 5
HWUSI-EAS645:1:1:4:2033#0/1 | NM_020991 | 5
HWUSI-EAS645:1:1:4:2033#0/2 | NM_022644 | 5
HWUSI-EAS645:1:1:4:2033#0/1 | NM_022644 | 5
HWUSI-EAS645:1:1:4:2033#0/2 | NM_022579 | 1
HWUSI-EAS645:1:1:4:2033#0/1 | NM_022579 | 1
HWUSI-EAS645:1:1:4:2033#0/1 | NM_001317 | 5
HWUSI-EAS645:1:1:4:2033#0/2 | NM_022640 | 5
HWUSI-EAS645:1:1:4:2033#0/1 | NM_022640 | 5
HWUSI-EAS645:1:1:4:2033#0/2 | NM_020991 | 5
HWUSI-EAS645:1:1:4:2033#0/1 | NM_020991 | 5
HWUSI-EAS645:1:1:4:2033#0/2 | NM_022644 | 5
HWUSI-EAS645:1:1:4:2033#0/1 | NM_022644 | 5
HWUSI-EAS645:1:1:4:2033#0/2 | NM_022579 | 1
HWUSI-EAS645:1:1:4:2033#0/1 | NM_022579 | 1
Look at the 7th column (3rd column in this case), the first line says we have 5 other similar alignments but there are only 4 other alignments from the same read and the last read says there is one other alignment, but where? Shouldn't bowtie print all other possible alignments with the -a command?
Does anyone know how to interpret this data?
Please help.
Thank you,
Kevin
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