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tophat2 -o tophat_fusion -p 15 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search hg19_bowtie1_index read_1.fastq read_2.fastq

I want to identify the circRNAS. But i am seeing error of Error running prep_reads. I have run this command for the alignment because I have used bowtie for indexing. Please see the picture it consists all input files and error results.

$ tophat2 -o tophat_fusion -p 9 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search genome_bowtie1_index p1r1.fq p1r2.fq 

[2022-06-19 20:48:31] Beginning TopHat run (v2.1.1)

-----------------------------------------------
[2022-06-19 20:48:31] Checking for Bowtie

          Bowtie version:    1.2.2.0

[2022-06-19 20:48:31] Checking for Bowtie index files (genome)..

[2022-06-19 20:48:31] Checking for reference FASTA file

[2022-06-19 20:48:31] Generating SAM header for genome_bowtie1_index

[2022-06-19 20:48:34] Preparing reads

    [FAILED]

Error running 'prep_reads'
circrnas tophat2 ciriexplorer2
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by HaroonPakistan • HaroonPakistan

Please, save the planet. don't post a screenshot when you can just copy-n-paste the text.

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written by Pierre Lindenbaum Pierre Lindenbaum

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