Genome updated, only have bam files, so reversed engineered bam to fastq with samtools. Realigning to the new genome build with bowtie2 with no special flags.
I get an error message like:
Error: Read <@DDD?D?@CFFE@4C@FFH@?+CHFGFBBBG*C;DFIEEFFB@BF@FEFFB=BFFECFA=CEEEIFCFFFB;;7;3?>>BBCC5>?;(,,2/2 has more read characters than quality values. libc++abi.dylib: terminating with uncaught exception of type int (ERR): bowtie2-align died with signal 6 (ABRT)
But then I check out that line, and it's the quality calls for a read. I changed the @ to A (one step up on the quality scale), and that solved the problem. For that read. A new read also has this problem. Is this really a systemic problem?