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

Question

[HaroonPakistan]

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'

[Pierre Lindenbaum]

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

[HaroonPakistan]

Thanks! I have updated.

[Pierre Lindenbaum]

• Tophat Prep_Reads Error
• Error running 'prep_reads' on TopHat (v2.0.9)
• what is the mean of 'Error running 'prep_reads' ???
• tophat Preparing reads [FAILED]