TopHat (v2.0.4)error

[fgh1124]

[2013-11-19 07:32:34] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2013-11-19 07:32:34] Checking for Bowtie
Bowtie version: 0.12.7.0
[2013-11-19 07:32:34] Checking for Samtools
Samtools version: 0.1.18.0
[2013-11-19 07:32:34] Checking for Bowtie index files
[2013-11-19 07:32:34] Checking for Bowtie index files
[2013-11-19 07:32:34] Checking for reference FASTA file
[2013-11-19 07:32:34] Generating SAM RNA_seq_suit/bowtie_index/mm9
format: fastq
quality scale: phred33 (default)
[2013-11-19 07:32:37] Reading known junctions from GTF file
[2013-11-19 07:32:43] Pre-filtering multi-mapped left reads
[2013-11-19 07:32:43] Mapping SRRXXX_1 to genome mm9 with Bowtie
[2013-11-19 10:21:54] Pre-filtering multi-mapped right reads
[2013-11-19 10:21:54] Mapping SRRXXX_2 to genome mm9 with Bowtie
[2013-11-19 13:34:48] Preparing reads
[FAILED]
Error running 'prep_reads'
Error: beginning of quality values record not found! (@831)

Thanks for your time!

[dpryan]

You might have a look at the read named @831. This suggests that there's something wrong with it.

[fgh1124]

You might have a look at the read named @831. This suggests that there's something wrong with it.

Thanks for your reply. UNfortunately, I could found the line started with "@831".