Yes, I have the same problem, I posted this in another thread:
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
I can get it working when using sorted SAM and sorted reference gene annotation to do quantification. But it seems declared too many nontest:
#Processed 22426 loci. [*************************] 100%
#Performed 4831 isoform-level transcription difference tests
#Performed 0 tss-level transcription difference tests
#Performed 3598 gene-level transcription difference tests
test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant
ENSCAFT00000000001 ENPP1 chr1:3251711-3321555 q1 q2 NOTEST 33.7819 1.42552 -3.16539 3.70202 0.000213891 no
ENSCAFT00000000003 - chr1:3363194-3365024 q1 q2 NOTEST 7.80975 3.21343 -0.888032 1.33992 0.180272 no
ENSCAFT00000000005 - chr1:3390440-3422494 q1 q2 NOTEST 0 0 0 0 1 no
ENSCAFT00000000006 PARD6G chr1:3508928-3565493 q1 q2 NOTEST 22.8188 0 6.95321e-310 2.22507e-308 0 no
It definitely should not be "NOTEST" with the FPKM values (26041 of 30913 isoforms are labeled as NOTEST").
But v0.9 did cut the de novo transcript prediction numbers a lot to about ~40000 from ~120,000. I am using single read data (84nt, 25M reads).
Comment
-
Originally posted by lshen View PostI can get it working when using sorted SAM and sorted reference gene annotation to do quantification. But it seems declared too many nontest:
#Processed 22426 loci. [*************************] 100%
#Performed 4831 isoform-level transcription difference tests
#Performed 0 tss-level transcription difference tests
#Performed 3598 gene-level transcription difference tests
test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant
ENSCAFT00000000001 ENPP1 chr1:3251711-3321555 q1 q2 NOTEST 33.7819 1.42552 -3.16539 3.70202 0.000213891 no
ENSCAFT00000000003 - chr1:3363194-3365024 q1 q2 NOTEST 7.80975 3.21343 -0.888032 1.33992 0.180272 no
ENSCAFT00000000005 - chr1:3390440-3422494 q1 q2 NOTEST 0 0 0 0 1 no
ENSCAFT00000000006 PARD6G chr1:3508928-3565493 q1 q2 NOTEST 22.8188 0 6.95321e-310 2.22507e-308 0 no
It definitely should not be "NOTEST" with the FPKM values (26041 of 30913 isoforms are labeled as NOTEST").
But v0.9 did cut the de novo transcript prediction numbers a lot to about ~40000 from ~120,000. I am using single read data (84nt, 25M reads).
The NOTEST status is set when there are fewer than (by default) 500 reads in that locus in both samples. You should be able to resolve this by lowering this threshold with the -c option.
Comment
-
Thank you, Cole. I also figured out it be this reason after I sent my comment.
I like this version especially in that it now predicts much fewer transcripts with my single read data. Now the total number of predicted transcripts is in the range of known annotated transcripts. I will check the new predictions for validity. Thank you for the hard working to get the tool quickly improved.
Comment
Latest Articles
Collapse
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
25 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
28 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
52 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment