Raw count matrix

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).

Quantification
was performed with SAMtools1 idxstats to generate the
quantification matrix.

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The matrix was
filtered with edgeR2 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.

File PRJNA628886_raw_quantification_206K.tsv.gz is the raw count matrix of the whole transcriptome.

File 76k_ids_list.txt is the identifier list of contigs expressed at 1 CPM in our conditions.

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1SAMtools
programs (view, sort, index and idxStats, flagstat): version 1.8,
standard parameters.

Ref:
Li, H. et al.
The Sequence Alignment/Map format and SAMtools.
Bioinformatics 25, 2078–2079
(2009).

2EdgeR:
version 3.26.5.

Ref: Robinson,
M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor
package for differential expression analysis of digital gene
expression data. Bioinformatics 26,
139–140 (2010).

Related to bioproject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA628886

本数据集的测序读段源自生物项目（BioProject）PRJNA628886，将其与参考转录组（生物项目PRJNA236528，https://doi.org/10.5061/dryad.11978）通过BWA-MEM算法（http://bio-bwa.sourceforge.net/bwa.shtml）完成比对。

定量分析采用SAMtools的idxstats工具完成，生成定量矩阵。

随后使用edgeR对该矩阵进行过滤，仅保留至少在1个样本中每百万序列计数（CPM，Count Per Million）大于1的重叠群（contigs），最终得到包含76,550个重叠群的定量矩阵。

文件PRJNA628886_raw_quantification_206K.tsv.gz为全转录组的原始计数矩阵。

文件76k_ids_list.txt为本实验条件下满足1 CPM表达阈值的重叠群标识符列表。

1. SAMtools工具套件（包含view、sort、index、idxStats、flagstat功能模块）：版本1.8，采用默认参数运行。
参考文献：Li, H. 等. 《序列比对/映射格式与SAMtools》. 生物信息学(Bioinformatics) 25, 2078–2079 (2009).
2. 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分析的Bioconductor工具包》. 生物信息学(Bioinformatics) 26, 139–140 (2010).

相关生物项目链接：https://www.ncbi.nlm.nih.gov/bioproject/PRJNA628886