Hi All,
My problem is that Bowtie is aligning paired ends together that shouldn't be.
The alignment uses the options, -m1 -v2 --best --strata -X800
The beginning of the alignment output looks fine...
Ex Output at top of file:
Id0001 + chr1 10000 sequence quality
Id0001 - chr1 10200 sequence quality
...
The end of the file seems to align reads together that don't go together (the input is highly repetitive, so this will still align)
Ex Output at bottom of file:
...
Id0052 + chr1 10000 sequence quality
Id0124 - chr1 10200 sequence quality
So it doesn't look like it's just outputting singletons for these reads, but is actually trying to align them together.
Importantly I've double checked that the two paired end inputs are matched. EVERY READ in the input is in the same location in the first paired end file as it's counter part in second paired end file!
Lastly, I'm still using Bowtie 1 so this isn't something weird with Bowtie 2.
Thanks ahead of time !!!!
My problem is that Bowtie is aligning paired ends together that shouldn't be.
The alignment uses the options, -m1 -v2 --best --strata -X800
The beginning of the alignment output looks fine...
Ex Output at top of file:
Id0001 + chr1 10000 sequence quality
Id0001 - chr1 10200 sequence quality
...
The end of the file seems to align reads together that don't go together (the input is highly repetitive, so this will still align)
Ex Output at bottom of file:
...
Id0052 + chr1 10000 sequence quality
Id0124 - chr1 10200 sequence quality
So it doesn't look like it's just outputting singletons for these reads, but is actually trying to align them together.
Importantly I've double checked that the two paired end inputs are matched. EVERY READ in the input is in the same location in the first paired end file as it's counter part in second paired end file!
Lastly, I'm still using Bowtie 1 so this isn't something weird with Bowtie 2.
Thanks ahead of time !!!!
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