Hi, i want to map the single-end short reads to the genome.
first, i map the reads to the genome with bowtie.
second, for the unaligned reads, i want to map it across the annotation file. i download the GTF file from UCSC.
tophat -G ~/GFF3/ce6-sangerGene.gtf /ws190_index/C.elegans.ws190.dna unaligned.txt
but failed.
could anyone help to solve this problem?
first, i map the reads to the genome with bowtie.
second, for the unaligned reads, i want to map it across the annotation file. i download the GTF file from UCSC.
tophat -G ~/GFF3/ce6-sangerGene.gtf /ws190_index/C.elegans.ws190.dna unaligned.txt
but failed.
could anyone help to solve this problem?
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