Bowtie Error Message

[cutcopy11]

Hello,

I am trying to map some human reads with Bowtie, and after running the program, I received the message below and did not obtain statistics for mapping. It did apparently map 77.5 million reads with the options added (I did a line count on the output file), but I am not sure if Bowtie finished mapping the reads. The input fastq file came from SRA. I have the most recent version of Bowtie for Linux. Does anyone have any suggestions on how to avoid this error so that Bowtie finishes mapping the reads?

$ ./bowtie -a -v 2 -m 3 hg19_c -C -q --suppress 1,6,7,8 invitro_1.fastq >invitro_1_mapped.txt

Saw ASCII character -1 but expected 33-based Phred qual.
Command: ./bowtie -a -v 2 -m 3 -C -q --suppress 1,6,7,8 hg19_c invitro_1.fastq

Thanks,
Clayton

[holywoool]

Bowite has many options for different formats of quality score,the default is --phred33-quals,which means the inputs(quality scores) are taken as ASCII characters.
However,it seems that your RNA-Seq data were SOLiD color space format,and usually SOLiD platforms output quality scores in integer.
So,try this option "--integer-quals" instead of the default one,I think that is the problem.