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. 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 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. p { margin-bottom: 0.25cm; direction: ltr; line-height: 120%; text-align: left; orphans: 2; widows: 2 } a:link { color: #0000ff } 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