Raw count matrix
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Reads from Bioproject PRJNA628886 where aligned against reference transcriptome (Bioproject PRJNA236528, https://doi.org/10.5061/dryad.11978) with BWA mem (http://bio-bwa.sourceforge.net/bwa.shtml). <br>Quantification was performed with SAMtools<sup>1</sup> idxstats to generate the quantification matrix. p { margin-bottom: 0.25cm; direction: ltr; line-height: 120%; text-align: left; orphans: 2; widows: 2 } a:link { color: #0000ff } The matrix was filtered with edgeR<sup>2</sup> and only contigs with more than 1 CPM (Count Per Million) in at least one sample were kept, providing a matrix of 76,550 contigs. <br>File <b>PRJNA628886_raw_quantification_206K.tsv.gz </b>is the raw count matrix of the whole transcriptome. <br> File <b>76k_ids_list.txt</b> is the identifier list of contigs expressed at 1 CPM in our conditions. <br><br> p { margin-bottom: 0.25cm; direction: ltr; line-height: 120%; text-align: left; orphans: 2; widows: 2 } a:link { color: #0000ff } <sup>1</sup>SAMtools programs (view, sort, index and idxStats, flagstat): version 1.8, standard parameters. <i>Ref: Li, H. </i><i>et al.</i><i> </i><i>The Sequence Alignment/Map format and SAMtools. </i><i>Bioinformatics</i><i> </i><i><b>25</b></i><i>, 2078–2079 (2009).</i> <sup>2</sup>EdgeR: version 3.26.5. <i>Ref: Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. </i><i>Bioinformatics</i><i> </i><i><b>26</b></i><i>, 139–140 (2010).</i><i><br></i>Related to bioproject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA628886
本数据集的测序读段（Reads）来自生物项目（Bioproject）PRJNA628886，使用BWA mem（http://bio-bwa.sourceforge.net/bwa.shtml）将读段比对至参考转录组（对应生物项目PRJNA236528，DOI: 10.5061/dryad.11978）。<br>使用SAMtools<sup>1</sup>的idxstats工具进行定量分析，生成定量矩阵。 使用edgeR<sup>2</sup>对上述定量矩阵进行过滤，仅保留至少在1个样本中计数每百万（CPM, Count Per Million）大于1的重叠群（contigs），最终得到包含76550个重叠群的过滤后矩阵。<br>文件**PRJNA628886_raw_quantification_206K.tsv.gz**为全转录组的原始计数矩阵。<br>文件**76k_ids_list.txt**为本研究条件下CPM≥1的表达重叠群的标识符列表。<br><br> <sup>1</sup>SAMtools工具集（包含view、sort、index、idxStats及flagstat功能）：版本1.8，采用标准参数。参考文献：Li, H. 等。《Sequence Alignment/Map格式与SAMtools》，《Bioinformatics》，25卷，2078–2079 (2009)。<br> <sup>2</sup>edgeR：版本3.26.5。参考文献：Robinson, M. D., McCarthy, D. J. & Smyth, G. K.《edgeR：用于数字基因表达数据差异表达分析的Bioconductor工具包》，《Bioinformatics》，26卷，139–140 (2010)。<br> 相关生物项目：https://www.ncbi.nlm.nih.gov/bioproject/PRJNA628886
