I am using tophap with solid single-end data.
the command line is :
tophat --color --quals -p 8 -o $outdir --library-type fr-secondstrand -G $gtffile hg19 $reads $qual
it reports the error message:
Error: you must set the mean inner distance between mates with -r
but -r is only for paired-end data, so I don't know what should I do.
the command line is :
tophat --color --quals -p 8 -o $outdir --library-type fr-secondstrand -G $gtffile hg19 $reads $qual
it reports the error message:
Error: you must set the mean inner distance between mates with -r
but -r is only for paired-end data, so I don't know what should I do.
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