Closed whelena closed 4 years ago
Hi @hkanya, unless there is a systematic problem with the format of your gene list file, it's likely that a subset of MGI IDs couldn't be mapped to an HGNC ID. GeneWalk will print a warning for each specific case but otherwise proceed with the analysis. The example you posted (MGI:894679) looks mappable to me, do you have specific examples of ones that couldn't be mapped, and for which you got a warning?
Some expected numbers to compare your run with: we found that for ~5% of our 1861 input MGI ids no human HGNC ids were found in our study of mouse RNA-seq (see biorxiv paper for details). Hope this helps you interpret your results.
I used 851 mouse genes and I'm not sure how many of them were unmappable but the genewalk_result.csv file is empty.
The genewalk_all.log looks something like this: WARNING: [2019-09-11 10:33:06] genewalk.gene_lists - Could not get HGNC ID for MGI ID "MGI:3644854" WARNING: [2019-09-11 10:33:06] genewalk.gene_lists - Could not get HGNC ID for MGI ID "MGI:1926387" WARNING: [2019-09-11 10:33:06] genewalk.gene_lists - Could not get HGNC ID for MGI ID "MGI:1920198" WARNING: [2019-09-11 10:33:06] genewalk.gene_lists - Could not get HGNC ID for MGI ID "MGI:2141599" WARNING: [2019-09-11 10:33:06] genewalk.gene_lists - Could not get HGNC ID for MGI ID "MGI:1916394" WARNING: [2019-09-11 10:33:06] genewalk.gene_lists - Could not get HGNC ID for MGI ID "MGI:1916672" WARNING: [2019-09-11 10:33:06] genewalk.gene_lists - Could not get HGNC ID for MGI ID "MGI:1923724" WARNING: [2019-09-11 10:33:06] genewalk.gene_lists - Could not get HGNC ID for MGI ID "MGI:103582" WARNING: [2019-09-11 10:33:06] genewalk.gene_lists - Could not get HGNC ID for MGI ID "MGI:1354731" WARNING: [2019-09-11 10:33:06] genewalk.gene_lists - Could not get HGNC ID for MGI ID "MGI:2449316" WARNING: [2019-09-11 10:33:06] genewalk.gene_lists - Could not get HGNC ID for MGI ID "MGI:2444923" WARNING: [2019-09-11 10:33:06] genewalk.gene_lists - Could not get HGNC ID for MGI ID "MGI:1098583"
It seems your input file contains the gene ids with quotations "", for example "MGI:3644854". I checked our code and currently that is the reason why all of your genes don't map. For now, I would advice you to use a list without the quotations and try again. If you are getting the gene list from R, then you can use quote=FALSE to do this: for example write.table(mgi_list, file = file_name,row.names=FALSE,col.names=FALSE,quote=FALSE)
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I tried that and I am still receiving the same error, do I need to convert it into human genes in R before using it on genewalk?
error: WARNING: [2019-09-12 10:53:13] genewalk.gene_lists - Could not get HGNC ID for MGI ID 1921920 WARNING: [2019-09-12 10:53:13] genewalk.gene_lists - Could not get HGNC ID for MGI ID 3643362 WARNING: [2019-09-12 10:53:13] genewalk.gene_lists - Could not get HGNC ID for MGI ID 3643618 WARNING: [2019-09-12 10:53:13] genewalk.gene_lists - Could not get HGNC ID for MGI ID 3781689 WARNING: [2019-09-12 10:53:13] genewalk.gene_lists - Could not get HGNC ID for MGI ID 3649964 WARNING: [2019-09-12 10:53:13] genewalk.gene_lists - Could not get HGNC ID for MGI ID 3642245
The output you are getting now is as expected. Note that many of the ids that previously failed are no longer in your log file (eg MGI:3644854) so they are properly mapped now. The remaining ones are mostly uncharacterized mouse genes, like pseudogenes / predicted genes (eg http://www.informatics.jax.org/marker/MGI:3643362) for which unfortunately no mapping to a human ortholog can be made reliably. See my message from yesterday: we had about 5% of our mouse genes not mapped because of that. In your case (851 input genes) that would be about 40-50 genes with a warning in your current log file. Can you see if that is about right? Also if you have a computer with 4 cores or access to a cluster, you can reduce the GeneWalk run time to 2-3hours and see your results file more quickly (see readme page for details): genewalk --project context1 --genes gene_list.txt --id_type mgi_id --nproc 4
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Okay, I'll see once the run is over. Thank you so much for your help!
Hi @hkanya, let us know if you are still having issues, otherwise I'll close this thread
It's working now thank you!
I have a text file of mouse genes with its MGI_ID (e.g. MGI:894679). However when I ran genewalk I receive errors : genewalk.gene_lists - Could not get HGNC ID for MGI ID although the code kept running. Is this an issue and if so should I convert the gene names into HGNC ID instead?