# how to replace these ID with official gene names? **URL:** \ **Category:** usegalaxy.org support\ **Tags:** uniprot, annotatemyids\ **Created:** [March 3, 2019, 9:50am UTC](https://help.galaxyproject.org/t/how-to-replace-these-id-with-official-gene-names/726 "2019-03-03T09:50:05Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![amir](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/amir/32/539_2.png) [@amir](https://help.galaxyproject.org/u/amir)\ **Post date:** [March 3, 2019, 9:50am UTC](https://help.galaxyproject.org/t/how-to-replace-these-id-with-official-gene-names/726/1 "2019-03-03T09:50:05Z")
im doing an rna seq analysis and after aligning with Star and filtering after Deseq2 a question remains. and that is:how to replace these ID with official gene names? i found a tool names annotatedmyIDs but it isnt working ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 4, 2019, 4:24pm UTC](https://help.galaxyproject.org/t/how-to-replace-these-id-with-official-gene-names/726/2 "2019-03-04T16:24:54Z")
The tool `annotateMyIDs` does have a small problem right now (all versions). The tool is not ignoring header lines even when that is set on the tool form. > [@AnnotateMyIDs Fatal error](https://help.galaxyproject.org/t/annotatemyids-fatal-error/701/4): > > **To use the tool now** , first run the tool `Remove beginning of a file` to remove the first line (header), then run the tool `annotateMyIds` . > [@AnnotateMyIDs Fatal error](https://help.galaxyproject.org/t/annotatemyids-fatal-error/701/5): > > ticket for the correction here if interested: [annotateMyIDs (several versions) is not really ignoring header line when option set · Issue #2319 · galaxyproject/tools-iuc · GitHub](https://github.com/galaxyproject/tools-iuc/issues/2319) Cross-reference post: [AnnotateMyIDs Fatal error](https://help.galaxyproject.org/t/annotatemyids-fatal-error/701) If that does not solve the problem, check that the `Organism` and `ID Type` are a match for the transcripts or genes in your data. The tool `UniProt ID mapping and retrieval` is an alternative for many use cases. Which tool to use depends on where the existing annotation was sourced (meaning: what ID content they currently represent). The format of the transcript/geneIDs can also cause problems. I’ve seen problems come up when a version is added to the end of the value – that should be removed before using either tool if present. Example: `NM_130786.2` should be modified to be `NM_130786`. If this does not address your issue, please share a few of the IDs and the source/genome build of the reference GTF used with whatever counting tool you used as input to `DESeq2`. We can probably help with determining the right starting “ID” type. ---
**Author:** ![amir](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/amir/32/539_2.png) [@amir](https://help.galaxyproject.org/u/amir)\ **Post date:** [March 5, 2019, 8:02am UTC](https://help.galaxyproject.org/t/how-to-replace-these-id-with-official-gene-names/726/3 "2019-03-05T08:02:12Z")
how i should remove the last part of my data ? im just want to try this and if it didnt work i will share my data ID and other information and my gtf.maybe im doing somethings wrong ---
**Author:** ![amir](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/amir/32/539_2.png) [@amir](https://help.galaxyproject.org/u/amir)\ **Post date:** [March 5, 2019, 8:08am UTC](https://help.galaxyproject.org/t/how-to-replace-these-id-with-official-gene-names/726/4 "2019-03-05T08:08:13Z")
how remove the last number ? NM\_130786.2 to `NM_130786`.??? ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 5, 2019, 4:59pm UTC](https://help.galaxyproject.org/t/how-to-replace-these-id-with-official-gene-names/726/5 "2019-03-05T16:59:32Z")
Hi - Since the identifier is in the first column, `Text transformation with sed` will work without a complex expression. Try this: ``` s/\.[0-9]+// ``` Other options include using regular expressions with tools like: - `Text reformatting with awk` - `Replace parts of text` - `Replace Text in entire line` - `Replace Text in a specific column` Or, if you don’t want to use a regular expression, the column can be isolated, the “dot” replaced with a “tab”, then all the data rearranged back again into one file. This could be put into a workflow if you plan to run it again. Example tool order: `Cut` \> `Convert delimiters to TAB` \> `Paste` \> `Cut`. Also, your IDs are _Emsembl transcripts_, so choose that as the input type with `annotateMyIDs`. Hope that helps! ---
**Author:** ![amir](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/amir/32/539_2.png) [@amir](https://help.galaxyproject.org/u/amir)\ **Post date:** [March 5, 2019, 3:02pm UTC](https://help.galaxyproject.org/t/how-to-replace-these-id-with-official-gene-names/726/6 "2019-03-05T15:02:45Z")
finaly it works thank you so much for your wonderfull support ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [September 23, 2022, 10:30pm UTC](https://help.galaxyproject.org/t/how-to-replace-these-id-with-official-gene-names/726/8 "2022-09-23T22:30:17Z")