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  • SpliceMap

    Hi

    I am trying SpliceMap for finding splicing in my reads. I have fastq formats (pair end- 2 files). I have reference genome in fasta format and gene annotation file as well. I have built bowtie index for my genome. But when i run SpliceMap, I am getting the following error

    ERROR: The following chromosome does not exist in the bowtie index
    1 | /home/mpimp-golm.mpg.de/matchado1334/Desktop/MonicaSteffi/Splicing_events/Tools/SpliceMap3352_linux-64/genome/chr.fa | pos:71 - 30812903
    Please make sure that all chromosomes are contained within the bowtie index


    I could not rectified this error. I tried so many times to rebuild bowtie index files using bowtie software and again i am getting these errors. Can anyone help me ?

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