Problem with reference ID type in Kallisto ouput file from EOA : Cannot use count file in EcoToxXplorer

ExpressAnalyst
1

Hi,
I’ve been using EOA to profile my RNAseq data for Japanese quail. The Kallsito output file gives me a strange reference ID for my sequences, for instance:

#Name
NC_029516.1_cds_XP_032301986.1_1
NC_029516.1_cds_XP_032301869.1_2
NC_029516.1_cds_XP_032301882.1_3

From what I understand the first part of the name is the chromosome ID and the 9 numbers after XP are the gene ID reference. The problem is that I want to use this data set in ecotoxXplorer but it cannot recognise the reference ID. In the past, the Kallisot output file from EOA gave ensembl ID name which was very easy to use with ecotoxXplorer. Would it be possible to have the same or another ref ID that would be directly usable in ecotoxXplorer.
Thanks for your help!
Paul

2

You will have to use ExpressAnalyst (not EcoToxXplorer) to analze the data.

We will fix this in the raw data processing to output the correct IDs, but you can address it right now by right clickign the count table, opening with Excel, going to the ‘Data’ tab, clicking the ‘Text to Columns’ button, using the “fixed width” setting, and clicking to separate where the XP_ starts. Here’s an example with a different file.

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Then you can delete the first column and upload as “RefSeq” ID type.

3

Looks like you will have to repeat the step to remove the “_1”, “_2”, etc from the end of the ID

4