I'm having a strange issue in which Tophat simply skips the reporting of output tracks - no errors thrown. The last entry in the run log is as follows:
/opt/tophat-2.0.9.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile Sal2_thout/tmp/right_kept_reads_seg10.bam.index --sam-header Sal2_thout/tmp/mm10_genome.bwt.samheader.sam - Sal2_thout/tmp/right_kept_reads_seg10.bam Sal2_thout/tmp/right_kept_reads_seg10_unmapped.bam
Run command was as follows:
tophat -p 8 --no-novel-juncs -o Sal2_thout Mmus_index/mm10 Sal2_1.fastq Sal2_2.fastq
There were only 2 million reads per dataset, so I doubt that this is an issue
/opt/tophat-2.0.9.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile Sal2_thout/tmp/right_kept_reads_seg10.bam.index --sam-header Sal2_thout/tmp/mm10_genome.bwt.samheader.sam - Sal2_thout/tmp/right_kept_reads_seg10.bam Sal2_thout/tmp/right_kept_reads_seg10_unmapped.bam
Run command was as follows:
tophat -p 8 --no-novel-juncs -o Sal2_thout Mmus_index/mm10 Sal2_1.fastq Sal2_2.fastq
There were only 2 million reads per dataset, so I doubt that this is an issue