Question: Crucial difference between dexseq and HTSeq-count
1
gravatar for igolkinaanna11
5.3 years ago by
igolkinaanna1110 wrote:

Hi everyone!

I decided to compare exon counts (DEXseq) and gene counts (HTSeq-count) for my alignments (done by STAR). Annotation(gtf) for mapping is just the same as that for counting. .gtf for DEXseq (modified by dexseq_prepare_annotation.py) a correspond to .gtf for HTSeq.
So everything seems ok, but I cannot interpret inconsistencies results. Under my hypothesis total count of exons should be somehow correlated with gene count. But what I see:

dexseq:
ENSG00000000003:001    248
ENSG00000000003:002    86
ENSG00000000003:003    63
ENSG00000000003:004    56
ENSG00000000003:005    66
ENSG00000000003:006    105
ENSG00000000003:007    91
ENSG00000000003:008    82
ENSG00000000003:009    80
ENSG00000000003:010    0
ENSG00000000003:011    16
ENSG00000000003:012    5
ENSG00000000003:013    0
ENSG00000000003:014    1
ENSG00000000003:015    2
ENSG00000000005:001    0
ENSG00000000005:002    0
ENSG00000000005:003    0
ENSG00000000005:004    0
ENSG00000000005:005    0
ENSG00000000005:006    0
ENSG00000000005:007    0
ENSG00000000005:008    0
ENSG00000000005:009    2

HTSeq-count:
ENSG00000000003    2
ENSG00000000005    2


Why it is too small for ENSG00000000003 in HTSeq-count?

Thank you for answers,
Anna.




 

rna-seq software error • 1.9k views
ADD COMMENTlink written 5.3 years ago by igolkinaanna1110

to have a better picture I would suggest you to plot all the gene vs exon counts in your data. that will tell you if what you observe for the first two genes is true for a vast amount of them or not. also, what is the total of the counts that you get in the two analyses? is it comparable?

ADD REPLYlink written 5.3 years ago by Martombo2.6k

I've done such plot (gene count vs total exon count per gene) and there is no correlation so I have the same situation is for vast majority of genes.

additional info from dexseq:
_ambiguous    752401
_empty    16077636
_lowaqual    0
_notaligned    0

additional info from HTSeq-count:
__no_feature    40579506
__ambiguous    44464
__too_low_aQual    0
__not_aligned    0
__alignment_not_unique    23644541

total counts form dexseq:
56934303

total counts from HTSeq:
65396229

ADD REPLYlink written 5.3 years ago by igolkinaanna1110
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