hi all,
i want to use bowtie for sort of paired end alignment, when i do;
bowtie.exe TESTTT -c CACCGAAAGACA,AGTAGCCACGGCGCAGCAACAC
it works fine, and i get two outputs.
However, when i do them in paired end mode;
bowtie.exe TESTTT -1 file1.txt -2 file2.txt
it doesn't work, since it generates no outputs. Someone knows how to generate such a file? Can it be a .fasta file?
Cheers,
Marten
i want to use bowtie for sort of paired end alignment, when i do;
bowtie.exe TESTTT -c CACCGAAAGACA,AGTAGCCACGGCGCAGCAACAC
it works fine, and i get two outputs.
However, when i do them in paired end mode;
bowtie.exe TESTTT -1 file1.txt -2 file2.txt
it doesn't work, since it generates no outputs. Someone knows how to generate such a file? Can it be a .fasta file?
Cheers,
Marten
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