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). <br>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. <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 } ¹SAMtools 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> ²EdgeR: version 3.26.5. <i>Ref: Robinson, M. D., McCarthy, D. J. &amp; 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