The test for cuffmerge

[fgh1124]

To whom it may concern,
Thanks for the excellent software. I have 8 mouse samples, and get the transcripts for each sample using cufflinks. When I use cuffmerge to merge each sample to one file, I met some mistakes: Just as the attachment, each sample expresses one transcripts named "NM_013633" or "NM_013633_ext", but I lost it in the merged file anf only left the short ones. I hope you can help me! I look forward to your reply!

ps: the attachment is the test data and the REANME file.
the default parameter "--max-bundle-length 3,500,000" is not suitable for mouse data. I advice adjust to "1,000,000,000".

Thanks for your time!

Best,

Guihai Feng

[fgh1124]

I need some advices.

I hope the seasoned men give me some advices.

[vpp605]

similar cuffmerge problem

I am having a similar problem, where I have transcripts that do not show up in my merged file. I can find the transcripts (and associated FPKM's) in both original gtf files that I am trying to merge, however in the final merged.gtf output from cuffmerge, they are no longer there. Any idea why this occurs? Is there some sort of filter that cuffmerge uses when it combines the gtf files?

Thanks!

[townway]

I also find the same problem, cuffmerge seems to filter some of the isoforms.

anybody here can help me ?
cuffmerge-*.tmap missing
I am running cuffmerge to combine some of samples GTF files. And error is showing as follow. If I make the .tmap my own, the output merged.gtf only has exon records but transcripts.

$ /usr/local/cufflinks/bin/cuffmerge -s /reference/hg19.fasta assembly_GTF_list.txt.txt

[Fri Jul 1 11:33:03 2011] Beginning transcriptome assembly merge
-------------------------------------------

[Fri Jul 1 11:33:03 2011] Preparing output location ./merged_asm/
Warning: no reference GTF provided!
[Fri Jul 1 11:33:03 2011] Converting GTF files to SAM
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[Fri Jul 1 11:33:03 2011] Assembling transcripts
cufflinks: /usr/lib64/libz.so.1: no version information available (required by cufflinks)
[bam_header_read] EOF marker is absent.
File ./merged_asm/tmp/mergeSam_fileaw7mto doesn't appear to be a valid BAM file, trying SAM...
[11:33:03] Inspecting reads and determining fragment length distribution.
Processed 121 loci. > Map Properties:
> Total Map Mass: 968.00
> Read Type: 173bp single-end
> Fragment Length Distribution: Gaussian (default)
> Estimated Mean: 246.97
> Estimated Std Dev: 52.49
[11:33:03] Assembling transcripts and estimating abundances.
Processed 121 loci. [Fri Jul 1 11:33:05 2011] Comparing against reference file None
Traceback (most recent call last):
File "/usr/local/cufflinks/bin/cuffmerge", line 573, in ?
sys.exit(main())
File "/usr/local/cufflinks/bin/cuffmerge", line 556, in main
compare_meta_asm_against_ref(params.ref_gtf, params.fasta, output_dir+"/transcripts.gtf")
File "/usr/local/cufflinks/bin/cuffmerge", line 410, in compare_meta_asm_against_ref
f_tmap = open(tmap)
IOError: [Errno 2] No such file or directory: './merged_asm/tmp_meta_asm.transcripts.gtf.tmap'

[ftorri]

Hi, sorry to bug with probably a naive question. I'm new to cufflinks. I am exploring all the tools. I have two main issues:
(1) I tried all the possible reference annotation files (refseq, UCSC, ensemble) but the output file of cufflinks (.gtf) doesn't have the gene_name even if for example the ensemble GTF files has it. SO my question is: how can I keep this info? Is it like that because you upload the file in UCSC without looking at it like a text file?

(2) If I have different samples (lets say brains of different people) and I want to evaluate the DE among them do I have to us ethe cuffmerge or the cuffcompare script?

Two examples:

-for tetsing I have one control brain and one affected brain: after having run cufflinks I have two transcipt.gtf. Do I have to use cuffcompare (to get a unique .gtf) and then cuffdiff?

-I will have four control brain and four affected brain, do I will have 8 transcripts.gtf files. Do I have to use cuffmerge grouping the 4 controls (producing one control.gtf file), the same for the cases (producing a cases.gtf). And then I have to use cuffcompare between the control.gtf and cases.gtf file having a unique .gtf file and then cuffdiff?

I don't understand if cuffmerge is to merge together ssample of the SAME groups and cuffcoimpare to unify different categories of samples..


thanks!!!


federica

[blue mood]

I have the same problem that some transcripts are lost in the cuffmerge output and the FPKM seems to be lower. Is there any solutions?