same transcript with different values in cuffdiff

Question: same transcript with different values in cuffdiff

4.0 years ago by

Canada

Ly, Dao • 20 wrote:

I'm have been searching on the forum but couldn't find answer for my specific question. I'm analyzing the cuffdiff of transcripts differential expression result and found that for some of the transcripts same accession number they have different values. I understand that gene has different isoforms but if the accession number is the same hence same isoform why would cuffdiff returns 2 different values. I'm including 2 examples of my cuffdiff output any explanation is greatly appreciated.

Thanks

example 1:

gene_id

gene

gene name

locus

status

value_1

value_2

log2(fold_change)

test_stat

p_value

q_value

significant

XLOC_000155	NM_014675	CROCC	chr1:17066807-17299474	OK	9.0882	3.96956	-1.19502	-2.3658	0.00085	0.007793	yes
XLOC_000155	NM_014675	CROCC	chr1:17066807-17299474	OK	0.899119	0.56106	-0.68036	-0.47306	0.5079	0.700695	no
XLOC_000155	NM_014675	CROCC	chr1:17066807-17299474	NOTEST	0.082748	0.13062	0.658588	0	1	1	no

example 2:

XLOC_000097	NM_001014765	FBXO44	chr1:11708417-11723384	OK	0.489105	0.789976	0.691666	0.084265	0.8371	0.913847	no
XLOC_000097	NM_183412	FBXO44	chr1:11708417-11723384	OK	1.08216	1.08248	0.000421	6.81E-05	0.97535	0.9858	no
XLOC_000097	NM_001014765	FBXO44	chr1:11708417-11723384	OK	1.65389	2.20919	0.41766	0.089671	0.90105	0.947527	no
XLOC_000097	NM_001014765	FBXO44	chr1:11708417-11723384	OK	2.1139	1.49908	-0.49583	-0.10367	0.88185	0.93797	no
XLOC_000097	NM_033182	FBXO44	chr1:11708417-11723384	OK	13.2691	19.5032	0.555641	0.317543	0.56475	0.74297	no
XLOC_000097	NM_183413	FBXO44	chr1:11708417-11723384	OK	28.9029	31.8086	0.1382	0.111997	0.84295	0.917138	no
XLOC_000098	NM_018438	FBXO6	chr1:11724149-11734409	OK	6.27812	7.10025	0.177536	0.327834	0.619	0.780796	no

rna-seq cuffdiff • 1.1k views

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modified 4.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.0 years ago by Ly, Dao • 20

I have the same problem. I use the Ensembl gtf file. I don't understand why this is happening.

ADD REPLY • link written 20 months ago by onemoreuser • 0

4.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Check the reference GTF dataset that you are using. Are the gene_id and transcript_id attributes assigned to the same value (transcript_id)? This can result from certain sources. Try using the one from iGenomes. A copy for hg19 is located on the public Main Galaxy server ready to use in 'Shared Data -> Data Libraries -> iGenomes'.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 4.0 years ago by Jennifer Hillman Jackson ♦ 25k

I'm having a similar problem and I downloaded the iGenomes files like you suggested, but the files that are supposed to be from NCBI don't look like NCBI to me. In the fasta files the chromosome is named '1', '2' and so on... these are not the NCBI chromosome names. I download the NCBI build37.2 for Mus Musculus.

ADD REPLY • link modified 20 months ago • written 20 months ago by onemoreuser • 0

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