tophat实用的工具

说明：tophat是基于bowtie的
fix_map_ordering: fix_map_ordering [--sam-header ] []
prep_reads:prep_reads [--filter-multi ] [,..] [ [,..]
bam2fastx: bam2fastx [--fasta|-a|--fastq|-q] [--color] [-Q] [--sam|-s|-t] [-M|--mapped-only|-A|--all] [-o ] [-P|--paired] [-N]
gtf_juncs: gtf_juncs
tophat-fusion-post: tophat-fusion-post [options]
bam_merge: bam_merge [-Q] [...]
gtf_to_fasta: gtf_to_fasta transcripts.gtf genome.fa out_file （gtf格式文件转化，也许用的上）
sam_juncs: sam_juncs
tophat_reports: tophat_reports        [right_map1,...,right_mapN] [right_reads.fq]
juncs_db:  juncs_db
segment_juncs: segment_juncs [right_reads.fq right_reads.bwtout right_seg1.bwtout,...,right_segN.bwtout]
contig_to_chr_coords: Takes the NCBI seq_contig file and maps contig coords to whole chromosome
coords in a GTF, GFF, or BED file
 contig_to_chr_coords.py
long_spanning_reads: long_spanning_reads [spliced_seg1.bwtout,...,spliced_segN.bwtout]
sra_to_solid: sra_to_solid input.fastq > output.fastq
map2gtf: map2gtf annotation.tlst alignments.bam out_file.bam
tophat:  tophat [options] [reads1[,reads2,...]] [quals1,[quals2,...]] [quals1[,quals2,...]]