Question: how to make an input file for DAVID Bioinformatics Tool for wheat's RNA seq data?
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gravatar for hirahameed222
10 months ago by
hirahameed2220 wrote:

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

rna-seq • 348 views
ADD COMMENTlink modified 10 months ago by jared.andrews075.0k • written 10 months ago by hirahameed2220
1

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.

ADD REPLYlink modified 10 months ago • written 10 months ago by Arup Ghosh2.2k

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

ADD REPLYlink modified 10 months ago • written 10 months ago by genomax78k
1
gravatar for jared.andrews07
10 months ago by
jared.andrews075.0k
St. Louis, MO
jared.andrews075.0k wrote:

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.

ADD COMMENTlink written 10 months ago by jared.andrews075.0k
0
gravatar for Giovanni.madrigal12
10 months ago by
Giovanni.madrigal12130 wrote:

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

ADD COMMENTlink written 10 months ago by Giovanni.madrigal12130
1

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.

ADD REPLYlink modified 10 months ago • written 10 months ago by genomax78k
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