How can i use bowtie to map solid data

[kentsing]

Dear Sir or Madam:
i am a fresh man to solid data and bowtie.
I try to aln my reads file to human genome wiith command:

"/data1/tools/bowtie-0.12.7/bowtie -q -p 6 -l 27 -n 2 -m 3 -e 950 -k 1 -S /data5/project/luo/index/Human_Genome SRR121550.fastq SRR121550.sam"

and get the following error message:
#################
Reads file contained a pattern with more than 1024 quality values.
Please truncate reads and quality values and and re-run Bowtie
##################

then i checked my fastq file and i found the fastq file contain the reads info like this

:@SRR121551.5 r1ahead05_20090410_1_cd4_5_8_1_32_149 length=35
T32222220222201131111312222111131212
+SRR121551.5 r1ahead05_20090410_1_cd4_5_8_1_32_149 length=35
!7;/&##%'&'#$''&$&/'-)-%#$#*&$1$%#%.

it's seems not a valid fastq file , but why??


I use the followling command to dump sra to fastq

/data1/tools/sratoolkit.2.1.9-centos_linux64/fastq-dump /data6/nuclesome/SRR155510.sra

pls help ! thx!!!

[bsuac6]

The bowtie command needs -C, as it is color space. Which is also why your reads are like this: T32222220222201131111312222111131212

Not sure if there are any other problems with your fastq file but I would try adding -C to the bowtie command and see if it works.