When running mapsplice2 I meet some problem.My command is like this:
python mapsplice.py -c Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/*.fa -x BowtieIndex/genome -1 BrM5.fastq
But it always said that
Error: -1 not specified
I have tried many methods but failed. Any reply will be thankful.
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zhangpeng1334880 •
I assume you are using single ended samples, I think you should be providing the directory to the reference fasta instead of specifying them, so by giving *.fa, it kind of disrupted the command? Maybe you should try:
python mapsplice.py -c Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/ -x BowtieIndex/genome -1 BrM5.fastq
Yes，I did it .It works well now.and the result is perfect.thanks a lot.
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