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Tophat err =1

Hello,

I am trying to align my RNAseq data to a reference genome, but it gives me this error message:

tophat2 -G Trihar1.gff Trihar1 Cd_C1.trimmomatic_out.fastq

  • [2017-09-09 15:27:34] Beginning TopHat run (v2.1.0)
  • [2017-09-09 15:27:34] Checking for Bowtie Bowtie version: 2.3.2.0
  • [2017-09-09 15:27:34] Checking for Bowtie index files (genome)..
  • [2017-09-09 15:27:34] Checking for reference FASTA file
  • [2017-09-09 15:27:34] Generating SAM header for Trihar1
  • [2017-09-09 15:27:34] Reading known junctions from GTF file Warning: TopHat did not find any junctions in GTF file
  • [2017-09-09 15:27:35] Preparing reads left reads: min. length=50, max. length=141, 24886332 kept reads (1026 discarded)
  • [2017-09-09 15:36:06] Building transcriptome data files ./tophat_out/tmp/Trihar1
  • [2017-09-09 15:36:06] Building Bowtie index from Trihar1.fa
  • [FAILED] Error: Couldn't build bowtie index with err = 1

GFF file and FA file are in the same directory with the same name. Also values in the first column of GFF file match the name of reference sequence in bowtie index.

rna-seq alignment tophat bowtie
• 157 views • link
written by Harumi • Harumi

Prior to running TopHat2, you have created the bowtie2 indices in this way:

bowtie2-build Trihar1.fa Trihar1

?

• 0 views • link
written by Kevin Blighe Kevin Blighe

Try the suggestion from post #8 from this SeqAnswers thread. In addition, maybe it would be helpful if you tell what are the sources of your fasta and gff.

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written by h.mon h.mon

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