Maplice2

Question

[zhangpeng1334880]

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.

Answer 1

[Sam]

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

[zhangpeng1334880]

Yes，I did it .It works well now.and the result is perfect.thanks a lot.