Okay, here is my attempt at a qucik perlscript to do this (see attachment). Hope some perl expert can make it less clumsy!
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Hello,
I am working with RNASEq data and we are to use 2 sets of 3 bam files each, i.e. 2 different conditions and 3 replicates per condition (which were obtained using Tophat2) with Cufflinks, Cuffmerge and finally Cuffdiff.
Cuffmerge requires a txt file with the full paths to the (in this case 6) transcripts.gtf files which was obtained on running cufflinks on each of the bam files. It also requires a reference genome fasta file and a gtf annotation file.
I chose to use gencode's latest version 'gencode.v12.annotation.gtf' with cuffmerge. I however am getting the following error, and I don't have an answer for it.
[Wed Jul 4 00:53:50 2012] Preparing output location ./merged_asm/
[Wed Jul 4 00:55:46 2012] Converting GTF files to SAM
[00:57:34] Loading reference annotation.
Error: duplicate GFF ID 'ENST00000361547.2' encountered!
[FAILED]
Error: could not execute gtf_to_sam
Traceback (most recent call last):
File "/share/apps/assembly/bin/cuffmerge", line 576, in ?
sys.exit(main())
File "/share/apps/assembly/bin/cuffmerge", line 554, in main
sam_input_files = convert_gtf_to_sam(gtf_input_files)
File "/share/apps/assembly/bin/cuffmerge", line 287, in convert_gtf_to_sam
sam_out = gtf_to_sam(line)
File "/share/apps/assembly/bin/cuffmerge", line 247, in gtf_to_sam
exit(1)
TypeError: 'str' object is not callable
Does anyone know what this means, or why it is happening? Can it be fixed? Any help would be greatly appreciated. Thanks
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