I am working with exomes from TCGA which are bam files. I am converting bam to fastq using SamToFastq by Picard and then realign the reads back to reference genome using another reference, not like in original bam files. With one file I get an error from Bowtie2:
Error, fewer reads in file specified with -2 than in file specified with -1
However Bowtie2 doesn't fall, it goes on running forever. Does anybody know how to solve this issue? I do not get such an error for other files I worked with from TCGA. I suppose that these unpaired reads should be simply ignored by Bowtie2.
Thanks in advance!