Hi I am trying to run dexseq_prepare_annotation.py on a gtf file (Ensembl version) downloaded from iGenomes. The organism is Arabidopsis thaliana. I am constantly getting error messages that look like this: Traceback (most recent call last): File "/home/as/R/x86_64-unknown-linux-gnu- library/3.0/DEXSeq/python_scripts/dexseq_prepare_annotation.py", line 51, in <module> for f in HTSeq.GFF_Reader( gtf_file ): File "/sw/python/2.7.1/lib/python2.7/site-packages/HTSeq-0.5.4p3-py2.7 -linux-x86_64.egg/HTSeq/__init__.py", line 221, in __iter__ ( attr, name ) = parse_GFF_attribute_string( attributeStr, True ) File "/sw/python/2.7.1/lib/python2.7/site-packages/HTSeq-0.5.4p3-py2.7 -linux-x86_64.egg/HTSeq/__init__.py", line 174, in parse_GFF_attribute_string raise ValueError, "The attribute string seems to contain mismatched quotes." ValueError: The attribute string seems to contain mismatched quotes. The command I used is: /home/as/R/x86_64-unknown-linux-gnu- library/3.0/DEXSeq/python_scripts/dexseq_prepare_annotation.py genes.gtf genes.flattened.gff I tried running the same script for other gtf files in the database (human, drosophila) and the script seems to work fine and the gtf files look comparable too (at a glance anyway) . Any help will be appreciated. A few lines from the gtf file Im using: 1 protein_coding exon 3631 3913 . + . exon_number "1"; gene_id "AT1G01010"; gene_name "ANAC001"; p_id "P20332"; seqedit "false"; transcript_id "AT1G01010.1"; transcript_name "AT1G01010.1"; tss_id "TSS22545"; 1 protein_coding CDS 3760 3913 . + 0 exon_number "1"; gene_id "AT1G01010"; gene_name "ANAC001"; p_id "P20332"; protein_id "AT1G01010.1"; transcript_id "AT1G01010.1"; transcript_name "AT1G01010.1"; tss_id "TSS22545"; 1 protein_coding start_codon 3760 3762 . + 0 exon_number "1"; gene_id "AT1G01010"; gene_name "ANAC001"; p_id "P20332"; transcript_id "AT1G01010.1"; transcript_name "AT1G01010.1"; tss_id "TSS22545"; 1 protein_coding CDS 3996 4276 . + 2 exon_number "2"; gene_id "AT1G01010"; gene_name "ANAC001"; p_id "P20332"; protein_id "AT1G01010.1"; transcript_id "AT1G01010.1"; transcript_name "AT1G01010.1"; tss_id "TSS22545"; I can send the complete file, need be. Thanks so much for your help. Anitha Sundararajan

Hi Anitha On 09/04/14 19:50, Anitha Sundararajan wrote: > ValueError: The attribute string seems to contain mismatched quotes. The A. thaliana GTF file contains a few rather strange gene names, which contain semicolons, and this confused previous versions of HTSeq. In the current version, this is fixed, so please update and try again. Simon