Hi all
I was following the instructions to analyze my RNASeq data with the DEXSeq package but I run into the following error while preparing the gff file:
/home/aleadam/R/x86_64-pc-linux-gnu-library/3.3/DEXSeq/python_scripts/dexseq_prepare_annotation.py", line 127, in <module>
assert l[i].iv.end <= l[i+1].iv.start, str(l[i+1]) + " starts too early"
AssertionError: <GenomicFeature: exonic_part 'ENSG00000166260+ENSG00000141198' at 17: 54951904 -> 54951900 (strand '-')> starts too early
I've seen a few posts with similar errors but never with the files downloaded from Ensembl itself, thus my post here.
I got the files from: ftp://ftp.ensembl.org/pub/release-89/gtf/homo_sapiens/
The command I run is:
python /home/aleadam/R/x86_64-pc-linux-gnu-library/3.3/DEXSeq/python_scripts/dexseq_prepare_annotation.py Homo_sapiens.GRCh38.89.gtf.gz Homo_sapiens.GRCh38.89.DEXSeq.gff
I do not know what "ENSG00000166260+ENSG00000141198" is. Is there something I'm doing wrong?
BTW, it happens with all the gtf files, and with version 88 as well. My apologies if this has been answered and I missed it. I'm struggling to understand what I'm doing here!
I was following the instructions to analyze my RNASeq data with the DEXSeq package but I run into the following error while preparing the gff file:
/home/aleadam/R/x86_64-pc-linux-gnu-library/3.3/DEXSeq/python_scripts/dexseq_prepare_annotation.py", line 127, in <module>
assert l[i].iv.end <= l[i+1].iv.start, str(l[i+1]) + " starts too early"
AssertionError: <GenomicFeature: exonic_part 'ENSG00000166260+ENSG00000141198' at 17: 54951904 -> 54951900 (strand '-')> starts too early
I've seen a few posts with similar errors but never with the files downloaded from Ensembl itself, thus my post here.
I got the files from: ftp://ftp.ensembl.org/pub/release-89/gtf/homo_sapiens/
The command I run is:
python /home/aleadam/R/x86_64-pc-linux-gnu-library/3.3/DEXSeq/python_scripts/dexseq_prepare_annotation.py Homo_sapiens.GRCh38.89.gtf.gz Homo_sapiens.GRCh38.89.DEXSeq.gff
I do not know what "ENSG00000166260+ENSG00000141198" is. Is there something I'm doing wrong?
BTW, it happens with all the gtf files, and with version 88 as well. My apologies if this has been answered and I missed it. I'm struggling to understand what I'm doing here!
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