I need a tool which can change the transcript id to ensemble or entraz ID ? i need it for goseq analysis, i think the problem in that tool is from the IDs. thanks

The mapping may not be 1-1. I would suggest using the Entrez IDs directly from Featurecounts instead to ensure distinct geneIDs. Then, at the end, you can convert those IDs to Ensembl for other purposes you may have. Follow the tutorial, it will help to avoid problems like this.

So how do i exactly redo the counting steps, which the Id, be gene instead of trascript ?

The counts are “by gene” when using Featurecounts with the default settings. And since your data is human, you could use the indexed hg38 genome and built-in annotation. “Transcriptomics” tutorials here go over the details, but I think you have seen those? Maybe review again and compare to your ste…

I did it with the default setting in featureCount. the Gene id looks like this. Geneid Length 100287102 1652 653635 1769 102466751 68 100302278 138 645520 1130 79501 918 729737 5474 102725121 1173 its not what ive been thinking

Hi @jennaj I used the default mode as you said and my geneID is like this : |Geneid|Length| | — | — | |100287102|1652| |653635|1769| |102466751|68| |100302278|138| |645520|1130| |79501|918| |729737|5474| |102725121|1173| are you sure this is working ? Goseq need ensembel ids and those are…

Right, these are Entrez IDs (expected). Map these to Ensembl with the tool: annotateMyIDs annotate a generic set of identifiers (Galaxy Version 3.7.0+galaxy1) After, rearrange the columns so that the Ensembl name replaces the Entrez name, and the file is back in the original format, with no extr…

Ok. it works. But about that Cut(table) you said, what should i put in field box to replace the Ensenbl ID and the counts back in the table, like the original format ? i think if i want to put the counts beside the Ensembel IDs, should i not using the tools like Join two dataset ?

@jennaj Hello Im still waiting for your respond. I know its close to Christmas and you are very busy .\ P.S Wish you the Best in 2020

Yes, you might need to join datasets based on common keys, cut/rearrange columns, plus add back in prior headers or create new ones. I haven’t been giving the full list of text manipulation tools, with exact steps, since you have been using Galaxy for a while now. Instead, more of an overview and p…

There’s also a one-step tool that can do this one task pretty well: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.7.0+galaxy1 or https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.7.0+galaxy1 dependi…

Right, that is what he is using after Featurecounts. But needs to reformat the results so can be used as inputs for goseq (counts and length data). Wants data using with Ensembl gene IDs instead of Entrez. I don’t think annotatemyIds will reformat/create outputs directly for goseq – or am I missing…