I am trying to align some paired end exome reads with bowti, but despite using the bow tie -q" switch to recognize fast file, I keep getting the error:
./bowtie -q -n -r -S -t -p 2 -I 0 -X 100 -ff --solexa1.3-quals indexes/hg19 -1 ~/Otogenetics_final_exome-original-110707_I327_FCB0AMFABXX_L3_index11_1.fastq.gz -2 ~/Otogenetics_final_exome-original-110707_I327_FCB0AMFABXX_L3_index11_2.fastq.gz bowtie.exome.sam
Time loading reference: 00:00:10
Time loading forward index: 00:00:18
Time loading mirror index: 00:00:14
Error: reads file does not look like a FASTA file
Seeded quality full-index search: 00:00:00
Time searching: 00:00:42
Overall time: 00:00:42
Same error when the files are unzipped. The fastq data look like:
@FCB0AMFABXX:3:1101:1497:2086#GGCTAAAT/1
TTACTTGCAAAGGAAAGACAATTTTGCATTACATGGGAACCAGCACATTTTCTGAATACACAGTTGTGGCTGGTATCTCTGTTGCTAAAA
+
gggggggdggdggdggggggggggggdggggggggggeggggggggegggegggeggggggeggggdefga`BBBBBBBBBBBBBBBBBB
@FCB0AMFABXX:3:1101:1378:2107#GGCTACAT/1
AATGCAGGAAGTGCTTCAAGGGAAATTTCTCACATTAAAAGCATATATTAGAACATTCAGGAGATCTAAAAGTCAATGCTCTAAGTTTCC
+
gggggggggggdggggggggggdggggggggdggggggggggggegdggdggfgegggefgcgeeegdacegbggfggfagggdgbfceT
Any ideas why bowtie will not accept the fastq format from Illumina Hiseq 2000 output?
./bowtie -q -n -r -S -t -p 2 -I 0 -X 100 -ff --solexa1.3-quals indexes/hg19 -1 ~/Otogenetics_final_exome-original-110707_I327_FCB0AMFABXX_L3_index11_1.fastq.gz -2 ~/Otogenetics_final_exome-original-110707_I327_FCB0AMFABXX_L3_index11_2.fastq.gz bowtie.exome.sam
Time loading reference: 00:00:10
Time loading forward index: 00:00:18
Time loading mirror index: 00:00:14
Error: reads file does not look like a FASTA file
Seeded quality full-index search: 00:00:00
Time searching: 00:00:42
Overall time: 00:00:42
Same error when the files are unzipped. The fastq data look like:
@FCB0AMFABXX:3:1101:1497:2086#GGCTAAAT/1
TTACTTGCAAAGGAAAGACAATTTTGCATTACATGGGAACCAGCACATTTTCTGAATACACAGTTGTGGCTGGTATCTCTGTTGCTAAAA
+
gggggggdggdggdggggggggggggdggggggggggeggggggggegggegggeggggggeggggdefga`BBBBBBBBBBBBBBBBBB
@FCB0AMFABXX:3:1101:1378:2107#GGCTACAT/1
AATGCAGGAAGTGCTTCAAGGGAAATTTCTCACATTAAAAGCATATATTAGAACATTCAGGAGATCTAAAAGTCAATGCTCTAAGTTTCC
+
gggggggggggdggggggggggdggggggggdggggggggggggegdggdggfgegggefgcgeeegdacegbggfggfagggdgbfceT
Any ideas why bowtie will not accept the fastq format from Illumina Hiseq 2000 output?
Comment