Cannot find any mention of reference gff/gtf annotations in cuffmerge output

[anna_vt]

Hi,

I have been using tophat and cufflinks to analyse some RNA seq data, but cuffmerge is not behaving as I would expect.

For all steps of the analysis I have used a reference gff3 file for RABT.

For tophat I specifed:

-G <gff file> --transcriptome-index <transcriptome prefix>

and on subsequent usage just

--transcriptome-index <transcriptome prefix>

For cufflinks I specified

--GTF-guide <gff file>

All the fpkm_tracking and gtf output files contain annotations from the original gtf file, including from transcripts with very high coverage so not just faux reads.

When using cuffmerge for the 16 samples I use the following command:

cuffmerge <cufflinks gtf list file> -o cuffmerge -g <gff file> -p 17

In none of the output files is there any mention of the annotations from the gff file.
I thought that the problem was that it is a gff file and not a gtf file, so I converted using

gffread <gff file> -T -o <gtf file>

cuffmerge <cufflinks gtf list file> -o cuffmerge -g <gtf file> -p 17

However the output is the same. There is also no mention of the gtf file in the log file for either gff3 or gtf:

/software/additional/bin/cuffmerge <path>/sam/tophat/cufflinks/gtfFileList.txt -o cuffmerge -g <path>/data/abH97_filt.gffread.gtf -p 17
gtf_to_sam -F <path>/sam/tophat/1_1/cufflinks/transcripts.1_1.gtf ./merged_asm/tmp/gtf2sam_filenEmb9h
gtf_to_sam -F <path>/sam/tophat/1_2/cufflinks/transcripts.1_2.gtf ./merged_asm/tmp/gtf2sam_fileeDtnvd
gtf_to_sam -F <path>/sam/tophat/1307_M5/cufflinks/transcripts.1307_M5.gtf ./merged_asm/tmp/gtf2sam_fileQhIpNd
gtf_to_sam -F <path>/sam/tophat/1_3/cufflinks/transcripts.1_3.gtf ./merged_asm/tmp/gtf2sam_fileAHuzXi
gtf_to_sam -F <path>/sam/tophat/2_1/cufflinks/transcripts.2_1.gtf ./merged_asm/tmp/gtf2sam_fileZw6YGs
gtf_to_sam -F <path>/sam/tophat/2_2/cufflinks/transcripts.2_2.gtf ./merged_asm/tmp/gtf2sam_file87N56G
gtf_to_sam -F <path>/sam/tophat/2_3/cufflinks/transcripts.2_3.gtf ./merged_asm/tmp/gtf2sam_file6ipSj0
gtf_to_sam -F <path>/sam/tophat/A151_M5/cufflinks/transcripts.A151_M5.gtf ./merged_asm/tmp/gtf2sam_file3SWsto
gtf_to_sam -F <path>/sam/tophat/F25_2_1/cufflinks/transcripts.F25_2_1.gtf ./merged_asm/tmp/gtf2sam_fileC2SotR
gtf_to_sam -F <path>/sam/tophat/F25_2_3/cufflinks/transcripts.F25_2_3.gtf ./merged_asm/tmp/gtf2sam_filelpirkp
gtf_to_sam -F <path>/sam/tophat/F25_2_4/cufflinks/transcripts.F25_2_4.gtf ./merged_asm/tmp/gtf2sam_fileJX9sR1
gtf_to_sam -F <path>/sam/tophat/F25_2_M5/cufflinks/transcripts.F25_2_M5.gtf ./merged_asm/tmp/gtf2sam_filezkS48I
gtf_to_sam -F <path>/sam/tophat/F25_2_M6/cufflinks/transcripts.F25_2_M6.gtf ./merged_asm/tmp/gtf2sam_file68Mb8u
gtf_to_sam -F <path>/sam/tophat/I142_4/cufflinks/transcripts.I142_4.gtf ./merged_asm/tmp/gtf2sam_file6CwbQl
gtf_to_sam -F <path>/sam/tophat/I142_M10/cufflinks/transcripts.I142_M10.gtf ./merged_asm/tmp/gtf2sam_fileeikjVg
gtf_to_sam -F <path>/sam/tophat/I142_M9/cufflinks/transcripts.I142_M9.gtf ./merged_asm/tmp/gtf2sam_filetTRVKg
sort -k 3,3 -k 4,4n --temporary-directory=./merged_asm//meta_asm_tmp/ ./merged_asm/tmp/gtf2sam_filenEmb9h ./merged_asm/tmp/gtf2sam_fileeDtnvd ./merged_asm/tmp/gtf2sam_fileQhIpNd ./merged_asm/tmp/gtf2sam_fileAHuzXi ./merged_asm/tmp/gtf2sam_fileZw6YGs ./merged_asm/tmp/gtf2sam_file87N56G ./merged_asm/tmp/gtf2sam_file6ipSj0 ./merged_asm/tmp/gtf2sam_file3SWsto ./merged_asm/tmp/gtf2sam_fileC2SotR ./merged_asm/tmp/gtf2sam_filelpirkp ./merged_asm/tmp/gtf2sam_fileJX9sR1 ./merged_asm/tmp/gtf2sam_filezkS48I ./merged_asm/tmp/gtf2sam_file68Mb8u ./merged_asm/tmp/gtf2sam_file6CwbQl ./merged_asm/tmp/gtf2sam_fileeikjVg ./merged_asm/tmp/gtf2sam_filetTRVKg > ./merged_asm/tmp/mergeSam_file1gh4tl
cufflinks -o ./merged_asm/ -F 0.05 -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 1 ./merged_asm/tmp/mergeSam_file1gh4tl
cuffcompare -o tmp_meta_asm -C -G  ./merged_asm//transcripts.gtf
cuffcompare -o tmp_meta_asm -C -G  ./merged_asm//merged.gtf

And nothing is prefixed / goes to the folder cuffmerge that i specifed with the -o flag, it only goes to the merged_asm folder.

Can anyone tell me what I am doing wrong or if this behaviour is as expected?
Version is: cufflinks v2.0.2

Many Thanks
Anna