Tophat colorspace problem --integer-quals 0
Hello everyone,
Is there an tophat option for setting the --integer-quals to 0 when using colorspace reads? I have a fastq file with phred33 quality. According to the manual when using the --color (or -C) option, the default of --integer-qual is set to 'yes'. There is no option to set the --integer-quals to zero, when I try --integer-qual 0, I retrieve the error: Error: Could not find Bowtie index files (0.*.ebwt).
When executing tophat, this is my output, which many people on this forum have when using colorspace, but noone has a solution:
When reading this output, Tophat recognized the phred33 quality scale but it wants a FASTQ-int file...
Anyone knows how to solve this error?
[EDIT]
Tried to use tophat with the --integer-quals, but then already stucking at prep_reads: terminate called after throwing an instance of 'int'
[EDIT]
Now tried to convert the fastq reads to integer-quals quality's, but then I get the error:
Did anyone use fastq files from a solid sequencer on tophat? How did your files look?
Is there an tophat option for setting the --integer-quals to 0 when using colorspace reads? I have a fastq file with phred33 quality. According to the manual when using the --color (or -C) option, the default of --integer-qual is set to 'yes'. There is no option to set the --integer-quals to zero, when I try --integer-qual 0, I retrieve the error: Error: Could not find Bowtie index files (0.*.ebwt).
When executing tophat, this is my output, which many people on this forum have when using colorspace, but noone has a solution:
Code:
[2013-03-18 10:42:01] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-03-18 10:42:01] Checking for Bowtie
Bowtie version: 0.12.8.0
[2013-03-18 10:42:01] Checking for Samtools
Samtools version: 0.1.14.0
[2013-03-18 10:42:01] Checking for Bowtie index files
[2013-03-18 10:42:01] Checking for Bowtie index files
[2013-03-18 10:42:01] Checking for reference FASTA file
[2013-03-18 10:42:01] Generating SAM header for /home/sge_share_fedor12/jetse/GENOMES/GRCh37_gatk/GRCh37_gatk_colorspace
format: fastq
quality scale: phred33 (default)
[2013-03-18 10:42:16] Reading known junctions from GTF file
[2013-03-18 10:42:42] Preparing reads
left reads: min. length=49, max. length=49, 99681 kept reads (319 discarded)
[2013-03-18 10:42:44] Using pre-built transcriptome index..
[2013-03-18 10:42:56] Mapping left_kept_reads to transcriptome human_GRCh37_gatk_index with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read: 7T0@
are you sure this is a FASTQ-int file?
Command: /usr/bin/bowtie -q -C --col-keepends -v 3 -k 1 -m 1 -S -p 1 --sam-nohead --max /dev/null /home/sge_share_fedor12/jetse/GENOMES/GRCh37_gatk/human_GRCh37_gatk_index -
Anyone knows how to solve this error?
[EDIT]
Tried to use tophat with the --integer-quals, but then already stucking at prep_reads: terminate called after throwing an instance of 'int'
[EDIT]
Now tried to convert the fastq reads to integer-quals quality's, but then I get the error:
Code:
Error encountered parsing file /home/sge_share_fedor12/jetse/wntSignalling/test/splitted/p1.A3754971/p1.A3754971_0_F3.fastq: Length mismatch between sequence and quality strings for A3754971_F3_0001_0 (49 vs 146).