Error Happened When Using Tophat To Run On The One-End Of Paired-End Rna-Seq Data

Question

[zhouchan99]

I have paired-end RNA-seq data: End1.fastq and End2.fastq. Tophat ran well on the two ends "tophat [path-to-reference-genome] End1.fastq End2.fastq", but if I tried to let tophat run on each end of RNA-seq data separately, it failed. My command is like "tophat [path-to-reference-genome] End1.fastq", then the terminal replied as follows:

-----------------------------------------------
[2014-03-03 13:36:35] Beginning TopHat run (v2.0.8)
[2014-03-03 13:36:35] Checking for Bowtie
          Bowtie version:     2.1.0.0
[2014-03-03 13:36:35] Checking for Samtools
        Samtools version:     0.1.18.0
[2014-03-03 13:36:35] Checking for Bowtie index files
[2014-03-03 13:36:35] Checking for reference FASTA file
[2014-03-03 13:36:35] Generating SAM header for /XXXX/hg19
Traceback (most recent call last):
  File "/apps/source/tophat-2.0.8/tophat-2.0.8.Linux_x86_64/tophat", line 4030, in <module>
    sys.exit(main())
  File "/apps/source/tophat-2.0.8/tophat-2.0.8.Linux_x86_64/tophat", line 3885, in main
    params.read_params = check_reads_format(params, reads_list)
  File "/apps/source/tophat-2.0.8/tophat-2.0.8.Linux_x86_64/tophat", line 1822, in check_reads_format
    zf = ZReader(f_name, params)
  File "/apps/source/tophat-2.0.8/tophat-2.0.8.Linux_x86_64/tophat", line 1775, in __init__
    self.file=open(filename)**

Can tophat run on the single end data? If you know the reason, could you pls let me know? Many thanks!

[Devon Ryan]

Tophat can handle single-end files just fine. It looks like you just gave it a non-existent file name.

[zhouchan99]

Thanks! I am checking that.

[Sukhi Singh]

Did you sorted it, if yes, please post as an answer.