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imsharmanitin 07-28-2015 08:08 AM

Differential expression using TopHat/Cufflinks, analysis by CumeRbund
I am trying to do differential expression analysis for 6 samples with no replicates

The protocol used by me after following several threads and
is as follows

1) after steps like alignment, etc

2) I assembled transcripts for each sample
cufflinks -p 8 -o <output directory> accepted_hits.bam

5) Ran Cuffmerge to create a single merged transcriptome annotation:
cuffmerge -g Homo_sapiens.GRCh37.75.gtf -s Homo_sapiens.GRCh37.75.dna.primary_assembly.fa -p 8 assemblies.txt

6) ran cuffdiff using following options:
--library-type fr-unstranded
--dispersion-method blind -L C1,C2,C3,C4,C5,C6
-b ./index/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
-u ./merged_asm/merged.gtf

7) used CumeRbund for analysis

However, I was unable to get Ensemble id and instead got XLOC id for the genes.

following the thread
I tried following two options

1) featureNames(sigGenes)

tracking_id gene_short_name
1 XLOC_002638 HES4,RP11-54O7.17
2 XLOC_005270 <NA>
3 XLOC_005288 <NA>
4 XLOC_005368 <NA>
5 XLOC_007367 RP11-47A8.5
6 XLOC_007664 <NA>
7 XLOC_007703 <NA>

But the names for some of XLOC were missing

2) then i tired other method and i got error

> names<-featureNames(sigGenes)
> row.names(names)=names$tracking_id
> sigGenesNames <-as.matrix(names)
> sigGenesNames <- sigGenesNames [,-1]
> sigGenesData<-diffData(sigGenes)
> row.names(sigGenesData)= sigGenesData$gene_id
Error in `row.names<`(`*tmp*`, value = c("XLOC_002638", "XLOC_002638", :
duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names': ‘XLOC_002638’, ‘XLOC_005270’, [... truncated]

Hence, I started to look into the ways to get Ensemble ids and the threads lead to lot of confusion and queries.

  1. should i use gtf file crated by cuffmerge or cuffcompare as input for cuffdiff ?

  2. while creating database using cummerbund should we use genome and gtf file?

  3. If the answer of 2nd question is yes, then should I use gtf from Ensemble or cuffmerge or cuffcomapre?

  4. how to get Ensemble id instead of XLOC id.

  5. Is there some error in my protocol?

Thanks in advance.

csmatyi 08-17-2015 08:57 AM

Hello everybody,

I have a line from genes.fpkm_tracking from cuffdiff output:

XLOC_000001 - - XLOC_000001 NM_008866 TSS1 chr1:4807892-4846735 - - 18.3357 13.5137 23.1577 OK 18.0846 13.4121 22.7572 OK

Here the aggregated control sample value is 18.3357

However, from the 3 control transcript.gtf files I have these 3 values:

../Nsg1-Hip_tophat/cufflinks_output_gtf/genes.fpkm_tracking:NM_008866 - - NM_008866 - - chr1:4807892-4846735 - - 16.1344 13.3363 18.9325 OK
../Nsg2-Hip_tophat/cufflinks_output_gtf/genes.fpkm_tracking:NM_008866 - - NM_008866 - - chr1:4807892-4846735 - - 15.4661 12.8039 18.1283 OK
../Nsg3-Hip_tophat/cufflinks_output_gtf/genes.fpkm_tracking:NM_008866 - - NM_008866 - - chr1:4807892-4846735 - - 13.0078 10.6329 15.3827 OK

Here the aggregete value of 18.3 is larger than the individual values 16.1, 15.5, and 13.0. How does cuffdiff calculate the aggregate values from the 3 samples?
Does it normalize? How does it do so?

I've tried finding this in the Trapnell, 2012 Nature Protocol paper, but it doesn't say.

Thanks, csmatyi

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