cufflinks tophat 资料

 

（1）安装cufflinks tophat 
http://5527lok.blog.163.com/blog/static/6475158201242823917220/

（2）使用Tophat分析RNA-seq结果 
http://5527lok.blog.163.com/blog/static/647515820124525128349/

（3）从RNA-seq结果到差异表达 
http://5527lok.blog.163.com/blog/static/647515820124522629212/

（4）一个错误：

Reporting output tracks
       
[FAILED]

Error running /root/bin/tophat_reports
--min-anchor 8 --splice-mismatches 0 --min-report-intron 50
--max-report-intron 500000 --min-isoform-fraction 0.15
--output-dir C1_R2_thout/ --max-multihits 20 --max-seg-multihits 40
--segment-length 25 --segment-mismatches 2
--min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000
--min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50
--max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2
--read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3
--max-deletion-length 3 --bowtie1 -z gzip -p8 --inner-dist-mean 50 --inner-dist-std-dev 20
--gtf-annotations genes.gtf --gtf-juncs C1_R2_thout/tmp/genes.juncs --no-closure-search
--no-coverage-search --no-microexon-search --sam-header C1_R2_thout/tmp/genome_genome.bwt.samheader.sam
--report-discordant-pair-alignments --report-mixed-alignments --samtools=/root/bin/samtools
--bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5
--bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5
--bowtie2-ref-gap-cont 3 genome.fa C1_R2_thout/junctions.bed C1_R2_thout/insertions.bed C1_R2_thout/deletions.bed C1_R2_thout/fusions.out
C1_R2_thout/tmp/accepted_hits C1_R2_thout/tmp/left_kept_reads.m2g.bam,C1_R2_thout/tmp/left_kept_reads.m2g_um.mapped.bam,
C1_R2_thout/tmp/left_kept_reads.m2g_um.candidates.bam C1_R2_thout/tmp/left_kept_reads.bam C1_R2_thout/tmp/right_kept_reads.m2g.bam,
C1_R2_thout/tmp/right_kept_reads.m2g_um.mapped.bam,C1_R2_thout/tmp/right_kept_reads.m2g_um.candidates.bam C1_R2_thout/tmp/right_kept_reads.bam

Error: ReadStream::getRead() called with out-of-order id#!

错误原因：并行执行多个此类任务时，可能内存溢出。

该错误的讨论:

http://seqanswers.com/forums/showthread.php?t=15142
http://seqanswers.com/forums/showthread.php?t=21316
https://github.com/genome-vendor/tophat/blob/master/src/reads.cpp

 

（5）其他：

三种基因表达差异的显著性分析方法

http://5527lok.blog.163.com/blog/static/6475158201303032818276/

基因表达谱数据聚类分析相关内容 
http://5527lok.blog.163.com/blog/static/6475158201303032716731/

三种基因表达数据的分类分析方法  
http://5527lok.blog.163.com/blog/static/6475158201303032558460/