Hello SEQAnswers community!
Thank you for this wonderful community here and to those of who you donate your time to checking forum posts and helping those in need.. I'm hoping that someone might know a thing or two as to where I can look to troubleshoot a particular problem that I'm having.
I should say that there has been at least 3 other people with the same problem, albeit with different organisms.
My issue: I cannot get cuffdiff v2.1.1 to perform any splicing and promoter preference tests. I couldn't get the previous version of cuffdiff to do so either...
My pipeline is as follows: Map with TrueSight -> cufflinks -> cuffmerge -> cuffdiff
Here's the command line for cuffdiff:
I'm using the iGenomes gtf file and bowtie files for all analyses.
Here's the cuffdiff stdout:
Here's the first 10 lines of my splicing.diff file (promoters.diff looks about the same)
In a previous post, a user was able to get the splicing tests to work by rolling back to an older version of cufflinks (version 1.30) -- but given that there have been so many improvements to the software, I don't want to do this..
So at this point, I humbly ask if anyone might know how to remedy this? Is it a bug? Is there something about Arabidopsis that doesn't allow splicing tests to be completed?
Thank you immensely for your time and advice, I assure you, it is sincerely appreciated!!
Thank you for this wonderful community here and to those of who you donate your time to checking forum posts and helping those in need.. I'm hoping that someone might know a thing or two as to where I can look to troubleshoot a particular problem that I'm having.
I should say that there has been at least 3 other people with the same problem, albeit with different organisms.
My issue: I cannot get cuffdiff v2.1.1 to perform any splicing and promoter preference tests. I couldn't get the previous version of cuffdiff to do so either...
My pipeline is as follows: Map with TrueSight -> cufflinks -> cuffmerge -> cuffdiff
Here's the command line for cuffdiff:
Code:
cuffdiff -L OX,KO,WT -o cuffdiffed --FDR 0.1 -b bowtie/genome.fa -N -c 5 cuffmerged/merged.gtf truesight_OX_out/alignment.bam truesight_KO_out/alignment.bam truesight_WT_out/alignment.bam
Here's the cuffdiff stdout:
Code:
> Processed 30760 loci. [*************************] 100% Performed 85169 isoform-level transcription difference tests Performed 66792 tss-level transcription difference tests Performed 61458 gene-level transcription difference tests Performed 63795 CDS-level transcription difference tests Performed 0 splicing tests Performed 0 promoter preference tests Performing 0 relative CDS output tests Writing isoform-level FPKM tracking Writing TSS group-level FPKM tracking Writing gene-level FPKM tracking Writing CDS-level FPKM tracking Writing isoform-level count tracking Writing TSS group-level count tracking Writing gene-level count tracking Writing CDS-level count tracking Writing isoform-level read group tracking Writing TSS group-level read group tracking Writing gene-level read group tracking Writing CDS-level read group tracking Writing read group info Writing run info
Code:
test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant TSS1 XLOC_000001 ANAC001 1:3630-5899 OX KO NOTEST 0 0 0 0 1 1 no TSS10 XLOC_000007 GIF2 1:72338-74737 OX KO NOTEST 0 0 0.0384659 0 0.5459 1 no TSS100 XLOC_000083 PGP11 1:523650-528745 OX KO NOTEST 0 0 0 0 1 1 no TSS1000 XLOC_000884 LSH8 1:5785002-5785927 OX KO NOTEST 0 0 0 0 1 1 no TSS10000 XLOC_009107 AT2G13910 2:5837685-5839920 OX KO NOTEST 0 0 0 0 1 1 no TSS10001 XLOC_009108 AT2G13920 2:5844028-5845726 OX KO NOTEST 0 0 0 0 1 1 no TSS10002 XLOC_009109 AT2G13940 2:5852758-5857264 OX KO NOTEST 0 0 0 0 1 1 no TSS10003 XLOC_009110 AT2G13950 2:5857535-5859249 OX KO NOTEST 0 0 0 0 1 1 no TSS10004 XLOC_009111 AT2G13960 2:5859584-5861311 OX KO NOTEST 0 0 0 0 1 1 no
So at this point, I humbly ask if anyone might know how to remedy this? Is it a bug? Is there something about Arabidopsis that doesn't allow splicing tests to be completed?
Thank you immensely for your time and advice, I assure you, it is sincerely appreciated!!
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