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Incompatible Igenomes NCBI GRCh38 genes.gtf - gene_biotype annotation missing #460
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Indeed super annoying error, ran into the same problem, can be circumvented by supplying the |
Yes, apologies for this. It has indeed caused alot of confusion since the NCBI version of that genome was added. The fix that @leiendeckerlu is the best one for that version. I have been thinking about dropping that genome from |
Note: this has also been discussed at some length in #159 |
This has been added as warning here 1e752cb and will also auto-set |
This will now be auto-detected as of #603 such that featureCounts won't be run if the biotype field provided to the pipeline doesn't exist in the GTF file. This will now work for any GTF and not just those that were manually specified to generate a warning as mentioned in the above comment. |
Hi all,
I also try to work this around by running it with the gff from NCBI and a gff converted by gffread to gtf. There, normally the error is that the similar command returns something like
I think this is related to issue #92 from rsem. This is my current setup: revision 3.4, singularity, nextflow 21.05.0.edge. Side note, is only me or the link to get an invite to the slack channel does not work? I thank you very much for the help and the nice pipeline! |
Using iGenomes reference assembly and GTF turned out to be problematic. See here: https://nf-co.re/docs/usage/reference_genomes#illumina-aws-igenomes and here: nf-core/rnaseq#460 So instead we are now using the assembly and GTFs published by Ensembl
Using assemblies and GTFs from iGenomes turned out to be problematic. See here: https://nf-co.re/docs/usage/reference_genomes#illumina-aws-igenomes and here: nf-core/rnaseq#460 So instead we are now using the assembly and GTFs published by Ensembl.
Hello @LucasMS, did you manage to solve this problem? I running into the same one. I converted from gff3 to gtf, and receive the second of your two errors. |
@aaharonoff @LucasMS |
Hi @ aaharonoff , sorry! I do not remember how I solved or worked around this problem. I hope @berk1835 solution works for you. Cheers |
Hi,
I'm running into issues with the format of the genes.gtf which is referenced in v1.4.2 /conf/igenomes.config
The NCBI gtf does not include the gene_biotype field, so the pipeline fails in the feature_counts setting when using the default igenomes.config with the error message below. Can you point us to a valid gtf ?
S3 cmd to retrieve
genes.gtf
aws s3 --no-sign-request --region eu-west-1 sync s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/ /gnet/is5/p04/data/bioinfo/ehive/reference-data/igenomes/references/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/ --exclude "*" --include "genes.gtf"
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