problem with tRNAseq alignment

I am trying to align tRNAseq data to the tRNA transcriptom. I made the index files using bowtie and trying to align using tophat. when I run the program for a single file I got this error:

Warning: Empty fasta file: 'tophat_out/tmp/segment_juncs.fa' Warning: All fasta inputs were empty Error: Encountered internal Bowtie 2 exception (#1) Command: bowtie2-build --wrapper basic-0 tophat_out/tmp/segment_juncs.fa tophat_out/tmp/segment_juncs     [FAILED] Error: Splice sequence indexing failed with err =1

do you know how solve this problem?

rna-seq

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written 9.1 years ago by alirezamomeni707 •

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