Hi Everybody, I would like to analyse the fold change of RNAseq data. What is the best option to do it in excel?. I would like to compare samples FPKM values to determine the fold change. Thanks in advance. Bassam
Hello,
This post contains the formula for excel. If by chance you don't want the log2, the ratio itself is the fold change: https://www.researchgate.net/post/How_to_calculate_log2_fold_change_value_from_FPKM_value
If you are performing RNA-seq analysis in Galaxy, both Cuffdiff and Deseq2 calculate the log2 fold change value in the default output.
Galaxy tutorials: https://galaxyproject.org/learn/
Thanks, Jen, Galaxy team
Thanks so much. I got it. I would like to ask if I can get genes ID by group?. I mean if I am interested in apoptosis genes, cancer genes, or telomere genes, is there any way to obtain the genes in Excel or text-delimited format?. I hope my question is clear?. Thanks
Bassam
See the group Get Data for tools that pull data into Galaxy from several common data providers. Data from other sources can be loaded into Galaxy and used with many tools. The Galaxy 101 (found in the tutorial's link above) has examples of retrieving, grouping, joining, and filtering data from external sources.
Or you can use your genes in a list with tools in the group Phenotype Association to query functional annotation from public sources. Try DAVID or g:Profiler.
Tabular data can be manipulated within Galaxy and/or exported and used with external tools.
Thanks Jennifer. I used the list of genes I have to annotate the genes using DGI database option. Although I got some annotation but they don't include all genes and several annotated genes are repeated several times in the output list. Is there any limit for input gene list? or most probably, I am missing something?. Thanks again
Bassam
