MOESM4 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Additional file 4 Reference DE genes (all combinations): the archive contains four folders, one for each species (bos_taurus, capra_hircus, gallus_gallus, sus_scrofa). Each folder contains itself two subfolders, one for each model: diffcounts.nominsum (Model 1) and diffcounts.cdvsliver (Model 2). Results of Model 1 are given in:• refgenes.counts.min2tpm0.1.normcounts.diff.readme.idx• refgenes.counts.min2tpm0.1.normcounts.diff.cd4.cd8.bed• refgenes.counts.min2tpm0.1.normcounts.diff.cd4.liver.bed• refgenes.counts.min2tpm0.1.normcounts.diff.cd8.liver.bedResults of Model 2 are given in:• refgenes.counts.min2tpm0.1.normcounts.diff.readme.idxrefgenes.counts.min2tpm0.1.normcounts.diff.cd.liver.bed All bed files contain the coordinates and id of the genes found to be differentially expressed between the two conditions. The file also contains the normalized read counts of those genes in the different samples as well as the adjusted pvalue, logFC and normLogFC (see readme.idx file for more details).

附加文件4 差异表达参考基因（全组合版本）：该归档文件包含四个文件夹，分别对应四个研究物种：牛（Bos taurus）、山羊（Capra hircus）、家鸡（Gallus gallus）与猪（Sus scrofa）。每个物种文件夹下均设有两个子文件夹，分别对应两种分析模型：diffcounts.nominsum（模型1）与diffcounts.cdvsliver（模型2）。

模型1的结果文件如下：
• refgenes.counts.min2tpm0.1.normcounts.diff.readme.idx
• refgenes.counts.min2tpm0.1.normcounts.diff.cd4.cd8.bed
• refgenes.counts.min2tpm0.1.normcounts.diff.cd4.liver.bed
• refgenes.counts.min2tpm0.1.normcounts.diff.cd8.liver.bed

模型2的结果文件如下：
• refgenes.counts.min2tpm0.1.normcounts.diff.readme.idx
• refgenes.counts.min2tpm0.1.normcounts.diff.cd.liver.bed

所有BED格式文件（Browser Extensible Data）均收录了两种实验条件下存在差异表达的基因的基因组坐标与基因ID；此外，文件中还包含这些基因在不同样本中的标准化读段计数，以及校正后的p值、logFC与normLogFC（详细说明请参阅readme.idx文件）。