I am trying tophat to map pairend reads to the contigs and had some tophat sam files. but I found in all these sam files, the column7(RNEXT) is "=" or "*". that means the next segment is on the same contigs or unmapped. is this normatl?
my command is like this(I tried both tophat and tophat2):
tophat --segment-length 15 --keep-tmp --min-coverage-intron 30 --library-type fr-firststrand -r 2850 --no-convert-bam -o mydocuments 454AllContigs fastq_end1 fastq_end2
is there something I missed in my command? how can I find the next segment from the alignments?
Thanks
Xu
my command is like this(I tried both tophat and tophat2):
tophat --segment-length 15 --keep-tmp --min-coverage-intron 30 --library-type fr-firststrand -r 2850 --no-convert-bam -o mydocuments 454AllContigs fastq_end1 fastq_end2
is there something I missed in my command? how can I find the next segment from the alignments?
Thanks
Xu
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