Use Kellisto to map reads to cDNA and count

Kellisto is an ultrafast alignment-free quantification tool.

  1. Change parameters as indicated.

2. cDNA file can be obtained from the Solgenome.net(ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG3.0_release/ITAG3.0_cDNA.fasta) |

  1. Once you get the results, click on the “eye” icon on the history pane. Then click on the “disk” icon on the left bottom left-hand corner to download the data into your computer.
  2. Open the download file with Excel.

5. In Excel, click on “Data” and then click on “Text to Column”. Separate column using tab to separate data into columns. Sum the numbers in “est_counts” using Auto Sum function.