一、目的
比較stringtie 的merge 功能結(jié)果與cuffmerge結(jié)果差異
二、測(cè)試數(shù)據(jù)
2.1 物種:人類
2.2 測(cè)序類型: RNAseq
2.3 bam文件路徑: https://erp.novelbio.com/NBCWebApp/task_getTaskResultPage?taskId=573d62469c064f7b74984816
2.4 stringtie merge結(jié)果:https://erp.novelbio.com/NBCWebApp/task_getTaskResultPage?taskId=574ceaef60b2f463a158f41e
2.5 cuffmerge 文件結(jié)果路徑: https://erp.novelbio.com/NBCWebApp/task_getTaskResultPage?taskId=5743f3d17882a7d889085d1d
三、結(jié)果比較
3.1 數(shù)量統(tǒng)計(jì)
cuffmerge ERP 計(jì)算的FPKM結(jié)果中 有51213個(gè)基因;stringtie 的merge ballgown計(jì)算的FPKM有56427個(gè)基因;
共有的基因?yàn)?/span>18779個(gè)基因,cuffmerge特有32414個(gè)基因,stringtie merge特有37629個(gè)基因,共有基因數(shù)目少的原因是,新基因不同軟件命名方式不一樣。
3.2 使用IGV查看差異部分
stringtie merge輸出了有reads覆蓋的轉(zhuǎn)錄本(外顯子)
stringtie merge輸出了有reads覆蓋的轉(zhuǎn)錄本(外顯子)
無(wú)reads覆蓋的時(shí)候merge gtf應(yīng)該與參考的gtf一致
無(wú)reads覆蓋的時(shí)候merge gtf應(yīng)該與參考的gtf一致
結(jié)論:使用IGV查看兩個(gè)gtf的區(qū)別,大部分(約80%到90%)都是相同的,stringtie merge的結(jié)果相較于cuffmerge會(huì)準(zhǔn)確一些。
四、cuffmerge 結(jié)果gtf與stringtie merge結(jié)果gtf格式差異
4.1 cuffmerge結(jié)果
chr1 Cufflinks exon 11874 12227 . + . gene_id "XLOC_004584"; transcript_id "TCONS_00011998"; exon_number "1"; gene_name "DDX11L1"; oId "NR_046018.2"; nearest_ref "NR_046018.2"; class_code "="; tss_id "TSS6302";
chr1 Cufflinks exon 12613 12721 . + . gene_id "XLOC_004584"; transcript_id "TCONS_00011998"; exon_number "2"; gene_name "DDX11L1"; oId "NR_046018.2"; nearest_ref "NR_046018.2"; class_code "="; tss_id "TSS6302";
chr1 Cufflinks exon 13221 14409 . + . gene_id "XLOC_004584"; transcript_id "TCONS_00011998"; exon_number "3"; gene_name "DDX11L1"; oId "NR_046018.2"; nearest_ref "NR_046018.2"; class_code "="; tss_id "TSS6302";
4.2 stringtie merge結(jié)果
chr1 StringTie transcript 11874 14409 1000 + . gene_id "MSTRG.1"; transcript_id "NR_046018.2"; ref_gene_id "DDX11L1";
chr1 StringTie exon 11874 12227 1000 + . gene_id "MSTRG.1"; transcript_id "NR_046018.2"; exon_number "1"; ref_gene_id "DDX11L1";
chr1 StringTie exon 12613 12721 1000 + . gene_id "MSTRG.1"; transcript_id "NR_046018.2"; exon_number "2"; ref_gene_id "DDX11L1";
chr1 StringTie exon 13221 14409 1000 + . gene_id "MSTRG.1"; transcript_id "NR_046018.2"; exon_number "3"; ref_gene_id "DDX11L1";
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