Dear all,
I just installed the newest version of Bowtie2 (2.2.0)
The version appears to be incompatible with Tophat 2.0.10 (it cannot find bowtie2, even if it is in the PATH).
The problem arises from the fact that the executable bowtie2-align disappeared, as two executables substituted it: bowtie2-align-l and bowtie2-align-s
The Tophat problem can be fixed by putting in the path a link to bowtie2-align-l named bowtie2-align
My question is: what are the two versions -l and -s? The difference is not documented anywhere, but it's present also in the bowtie2-build executables.
I just installed the newest version of Bowtie2 (2.2.0)
The version appears to be incompatible with Tophat 2.0.10 (it cannot find bowtie2, even if it is in the PATH).
The problem arises from the fact that the executable bowtie2-align disappeared, as two executables substituted it: bowtie2-align-l and bowtie2-align-s
The Tophat problem can be fixed by putting in the path a link to bowtie2-align-l named bowtie2-align
My question is: what are the two versions -l and -s? The difference is not documented anywhere, but it's present also in the bowtie2-build executables.
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