how to make an input file for DAVID Bioinformatics Tool for wheat's RNA seq data?

Question

[hirahameed222]

Hi I am working on wheat RNA seq Data obtained via High Throughput Sequencing , as i am new to this work i am confused for input file required for DAVID > https://david-d.ncifcrf.gov/conversion.jsp?VFROM=NA. The nature protocol states about input file as:-

A list of gene identifiers is the only required input for all DAVID analytic modules or tools. The gene list may be derived from any type of high- throughput genomic, computational or proteomic study, such as DNA expression microarray, proteomics, CHIP-on-CHIP, SNP array, CHIP-sequence and so on.

It would be really helpful if someone has a Solution on How to produce input (list of gene identifiers) files for this tool.

Thanking in Advacne

[Arup Ghosh]

Align the data to the reference genome and then qualify transcripts and you can use the transcript list as an input list for DAVID analysis.

[GenoMax]

List of gene is a simple list. See this help page. You will need to ensure that the identifiers used work with DAVID.

Answer 1

[jared.andrews07]

DAVID has converters for practically any identifier you could have. You just have to tell it what to expect (Step 2: Select Identifier dropdown menu). However, I don't think it supports wheat.

You could try this tool, as it's more likely to have the proper annotations for wheat. I've never used it, but the layout looks similar to DAVID.

Answer 2

[Gio12]

A simple solution would be to BLAST your sequences, retrieve the gene ID's, and put them in a list.

[GenoMax]

hirahameed222 has RNAseq data and hopefully it has been aligned to and then counted against wheat reference genome with a standard set of identifiers from a GTF file.