Hi everyone. I am doing a RNA-seq project on tomato gene expression.
I am trying to convert my bam files to txt files by HTseq. My command is as follow:
htseq-count -f bam 31_36.bam ITAG2.4_de_novo_gene_finders.gff3 > 31_36.txt
and I encountered with the following error:
Error occured when processing GFF file (line 9 of file ITAG2.4_de_novo_gene_finders.gff3):
Feature SL2.50ch00_exon_1 does not contain a 'gene_id' attribute
[Exception type: ValueError, raised in count.py:53]
I have downloaded my gff3 file from https://solgenomics.net/ and the data belongs to tomato.
Could anyone tell me what is my problem and have it can be resolved?
Thank you very much
Hi Elyas,
Your Problem is 'gene-ID' in gff file, I guess it is better to get gff/gtf ftom Ensmbl or UCSC then run HTseq or you can remove / check line 9 to see what is difference with the rest.
Thank you very much Soheil Yousefi l have checked the lines but they are almost the same and at least differences are not detectable. So I tried to remove the lines that are mentioned in errors. But each time, new errors with a new line had come up gradually.
I have tried to find the gff3/gtf files from Ensemble and USCS but I am not sure if plant data is available in these sites.
I will check the FeaturCount in this case. I appreciate your suggestions.
- Badges
- Science topic
- Similar topics
- Filing