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Puriney's Notes

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[bio]常见差异表达分析方法概述  

2013-02-17 21:02:35|  分类: Bio |  标签: |举报 |字号 订阅

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RNA-seq reads were mapped to the human genome (build hg18) using TopHat 1.2.0 software

Differentially expressed genes: the number of reads mapped to each of the ensembl genes (release 54) was counted using the HTSeq python package, with the “union” overlap resolution mode, and –stranded=no. The R package DESeq v1.5.24 within the Bioconductor framework was used for differential expression analysis

Differentially expressed exons: non-overlapping exonic regions were defined using the “dexseq_prepare_annotation.py” script provided as part of the R DEXseq package. The number of reads falling in each of the defined exonic regions was counted using the DEXseq script “dexseq_count.py” with parameters -a=0 to include multi-reads mapped to different locations of the genome, and –stranded=no. Finally Differential expression analysis was done using the R package DEXSeq within the Bioconductor framework.

Differentially expressed introns: non-overlapping intronic regions which also don't overlap any exon on either strand were defined using an in-house script. (应该可以用我写的uniq_intron_producer.pl ) The number of reads falling in each of the defined regions was counted using a modified version of the “dexseq_count.py” DEXseq script , and differential expression analysis was done using the DESeqBioconductor package

Differentially expressed isoforms: Ensembl gtf file of all human genes (hg18 release 54) was re-processed using Cuffcompare v1.0.3 in order to add the missing tss_id and p_id attributes according to the user guide. The resulting gtf annotation file created by Cuffcompare was used as input to Cuffdiff v1.0.3 tool together with the fragment alignment files. Both Cuffcompare and Cuffdiff are part of the Cufflinks package

Genome_build: hg18
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