Cuffdiff problem

[ea11]

Hi,

I am attempting to run cuffdiff one some of my samples, using a custom gtf file that I created following the gtf file format, but I am having a problem running it. I am using cufflinks v2.2.1 and my code is:

cuffdiff -o /cuffdiff_treat1 -p 32 --library-type fr-firststrand custom.gtf files.bam files.bam 

However, this is the output I get:

You are using Cufflinks v2.2.1, which is the most recent release.
[11:49:06] Loading reference annotation.
Error parsing strand () from GFF line:
        3                                                        "";  "";  "";  ""; 

After removing line 3 from the gtf file, I still get the same error.

These are the first 10 lines of my gtf file, and I can't find what is wrong with it:

1       Cufflinks       exon    11745335        11745837        .       +       .       transcript_id "TCONS_00000870"; class_code "j"; gene_name "AGTRAP"; exon "1"; 
1       Cufflinks       exon    11747440        11747545        .       +       .       transcript_id "TCONS_00000870"; class_code "j"; gene_name "AGTRAP"; exon "2"; 
1       Cufflinks       exon    11748415        11748610        .       +       .       transcript_id "TCONS_00000870"; class_code "j"; gene_name "AGTRAP"; exon "3"; 
1       Cufflinks       exon    11750077        11751048        .       +       .       transcript_id "TCONS_00000870"; class_code "j"; gene_name "AGTRAP"; exon "4"; 
1       Cufflinks       exon    13488810        13488841        .       +       .       transcript_id "TCONS_00000995"; class_code "i"; gene_name "LRRC38"; exon "1"; 
1       Cufflinks       exon    13492785        13493144        .       +       .       transcript_id "TCONS_00000995"; class_code "i"; gene_name "LRRC38"; exon "2"; 
1       Cufflinks       exon    16455496        16455893        .       +       .       transcript_id "TCONS_00001210"; class_code "j"; gene_name "NECAP2"; exon "1"; 
1       Cufflinks       exon    16458835        16460078        .       +       .       transcript_id "TCONS_00001210"; class_code "j"; gene_name "NECAP2"; exon "2"; 
1       Cufflinks       exon    22025493        22025639        .       +       .       transcript_id "TCONS_00001445"; class_code "j"; gene_name "LINC00339"; exon "1"; 
1       Cufflinks       exon    22030280        22031279        .       +       .       transcript_id "TCONS_00001445"; class_code "j"; gene_name "LINC00339"; exon "2"; 

Any help would be much appreciated.

Thanks