Comments (8)
It seems to work on the test data, e.g.
idr --samples peak1 peak2 --verbose --rank q.value
returns output. What is the exact command that isnt working?
from idr.
Hi,
Perhaps I am doing something wrong, sorry - I tried the test files and it
does work. I'm using the command below (and have tried --rank p.value and
--rank signal.value) and get no peaks, but if I do not specify --rank I get
peaks ranked by signal.value (I can tell this from the output file because
columns 8 and 9 are set to -1).
idr --samples H3K4me3_rep1_callpeak_p1e-2_peaks.narrowPeak
H3K4me3_rep2_callpeak_p1e-2_peaks.narrowPeak -o
H3K4me3_IDR_rep1vsrep2_qvalue --idr-threshold 0.05 --rank q.value --plot
Here is the start of my dataset (peaks called in MACS2):
ABPA02001267 1279 2300 H3K4me3_rep1_callpeak_p1e-2_peak_1a 98 . 2.45547
9.83350 8.70161 225
ABPA02001267 1279 2300 H3K4me3_rep1_callpeak_p1e-2_peak_1b 174 . 3.16719
17.41792 15.97919 480
ABPA02001267 1279 2300 H3K4me3_rep1_callpeak_p1e-2_peak_1c 106 . 2.57598
10.66525 9.50756 895
ABPA02001268 251 793 H3K4me3_rep1_callpeak_p1e-2_peak_2 46 . 1.67656 4.65375
3.66030 328
ABPA02001273 332 620 H3K4me3_rep1_callpeak_p1e-2_peak_3 98 . 2.49152 9.80494
8.67419 164
ABPA02001282 72 1337 H3K4me3_rep1_callpeak_p1e-2_peak_4a 111 . 2.01017
11.19162 10.01817 524
ABPA02001282 72 1337 H3K4me3_rep1_callpeak_p1e-2_peak_4b 117 . 2.06141
11.76029 10.56994 854
ABPA02001286 16 946 H3K4me3_rep1_callpeak_p1e-2_peak_5a 202 . 2.46462
20.20859 18.61673 182
ABPA02001286 16 946 H3K4me3_rep1_callpeak_p1e-2_peak_5b 137 . 2.19984
13.73618 12.47353 504
ABPA02001287 102 993 H3K4me3_rep1_callpeak_p1e-2_peak_6a 103 . 2.13005
10.33780 9.19190 184
On 10 December 2015 at 13:04, Nathan Boley [email protected] wrote:
It seems to work on the test data, e.g.
idr --samples peak1 peak2 --verbose --rank q.value
returns output. What is the exact command that isnt working?
—
Reply to this email directly or view it on GitHub
#13 (comment).
Natalie Clare Silmon de Monerri
email: [email protected]
from idr.
Can you please send me a self contained test case?
On Thu, Dec 10, 2015 at 11:33 AM, Natalie Silmon de Monerri <
[email protected]> wrote:
Hi,
Perhaps I am doing something wrong, sorry - I tried the test files and it
does work. I'm using the command below (and have tried --rank p.value and
--rank signal.value) and get no peaks, but if I do not specify --rank I get
peaks ranked by signal.value (I can tell this from the output file because
columns 8 and 9 are set to -1).idr --samples H3K4me3_rep1_callpeak_p1e-2_peaks.narrowPeak
H3K4me3_rep2_callpeak_p1e-2_peaks.narrowPeak -o
H3K4me3_IDR_rep1vsrep2_qvalue --idr-threshold 0.05 --rank q.value --plotHere is the start of my dataset (peaks called in MACS2):
ABPA02001267 1279 2300 H3K4me3_rep1_callpeak_p1e-2_peak_1a 98 . 2.45547
9.83350 8.70161 225ABPA02001267 1279 2300 H3K4me3_rep1_callpeak_p1e-2_peak_1b 174 . 3.16719
17.41792 15.97919 480ABPA02001267 1279 2300 H3K4me3_rep1_callpeak_p1e-2_peak_1c 106 . 2.57598
10.66525 9.50756 895ABPA02001268 251 793 H3K4me3_rep1_callpeak_p1e-2_peak_2 46 . 1.67656
4.65375
3.66030 328ABPA02001273 332 620 H3K4me3_rep1_callpeak_p1e-2_peak_3 98 . 2.49152
9.80494
8.67419 164ABPA02001282 72 1337 H3K4me3_rep1_callpeak_p1e-2_peak_4a 111 . 2.01017
11.19162 10.01817 524ABPA02001282 72 1337 H3K4me3_rep1_callpeak_p1e-2_peak_4b 117 . 2.06141
11.76029 10.56994 854ABPA02001286 16 946 H3K4me3_rep1_callpeak_p1e-2_peak_5a 202 . 2.46462
20.20859 18.61673 182ABPA02001286 16 946 H3K4me3_rep1_callpeak_p1e-2_peak_5b 137 . 2.19984
13.73618 12.47353 504ABPA02001287 102 993 H3K4me3_rep1_callpeak_p1e-2_peak_6a 103 . 2.13005
10.33780 9.19190 184On 10 December 2015 at 13:04, Nathan Boley [email protected]
wrote:It seems to work on the test data, e.g.
idr --samples peak1 peak2 --verbose --rank q.value
returns output. What is the exact command that isnt working?
—
Reply to this email directly or view it on GitHub
#13 (comment).
Natalie Clare Silmon de Monerri
email: [email protected]
—
Reply to this email directly or view it on GitHub
#13 (comment).
from idr.
Hi,
Please find script and files attached - I think this is what you meant by a
self contained test? If not let me know and I'll send anything else.
Thank you!
On 10 December 2015 at 14:33, Natalie Silmon de Monerri <
[email protected]> wrote:
Hi,
Perhaps I am doing something wrong, sorry - I tried the test files and it
does work. I'm using the command below (and have tried --rank p.value and
--rank signal.value) and get no peaks, but if I do not specify --rank I get
peaks ranked by signal.value (I can tell this from the output file because
columns 8 and 9 are set to -1).idr --samples H3K4me3_rep1_callpeak_p1e-2_peaks.narrowPeak
H3K4me3_rep2_callpeak_p1e-2_peaks.narrowPeak -o
H3K4me3_IDR_rep1vsrep2_qvalue --idr-threshold 0.05 --rank q.value --plotHere is the start of my dataset (peaks called in MACS2):
ABPA02001267 1279 2300 H3K4me3_rep1_callpeak_p1e-2_peak_1a 98 . 2.45547
9.83350 8.70161 225ABPA02001267 1279 2300 H3K4me3_rep1_callpeak_p1e-2_peak_1b 174 . 3.16719
17.41792 15.97919 480ABPA02001267 1279 2300 H3K4me3_rep1_callpeak_p1e-2_peak_1c 106 . 2.57598
10.66525 9.50756 895ABPA02001268 251 793 H3K4me3_rep1_callpeak_p1e-2_peak_2 46 . 1.67656
4.65375 3.66030 328ABPA02001273 332 620 H3K4me3_rep1_callpeak_p1e-2_peak_3 98 . 2.49152
9.80494 8.67419 164ABPA02001282 72 1337 H3K4me3_rep1_callpeak_p1e-2_peak_4a 111 . 2.01017
11.19162 10.01817 524ABPA02001282 72 1337 H3K4me3_rep1_callpeak_p1e-2_peak_4b 117 . 2.06141
11.76029 10.56994 854ABPA02001286 16 946 H3K4me3_rep1_callpeak_p1e-2_peak_5a 202 . 2.46462
20.20859 18.61673 182ABPA02001286 16 946 H3K4me3_rep1_callpeak_p1e-2_peak_5b 137 . 2.19984
13.73618 12.47353 504ABPA02001287 102 993 H3K4me3_rep1_callpeak_p1e-2_peak_6a 103 . 2.13005
10.33780 9.19190 184On 10 December 2015 at 13:04, Nathan Boley [email protected]
wrote:It seems to work on the test data, e.g.
idr --samples peak1 peak2 --verbose --rank q.value
returns output. What is the exact command that isnt working?
—
Reply to this email directly or view it on GitHub
#13 (comment).
Natalie Clare Silmon de Monerri
email: [email protected]
Natalie Clare Silmon de Monerri
email: [email protected]
from idr.
I dont see an attachment.
from idr.
Sorry here: test.zip
from idr.
It looks like the code is working - it's just that no peaks pass the 5% IDR threshold when using the q value ranking. Try using --soft-idr-threshold instead of --idr-threshold and then you can see all of the peaks and their idr values.
from idr.
ok, I'll try that. Thank you!
from idr.
Related Issues (20)
- Empty merged picks list HOT 2
- Order of Peak1 vs. Peak2 after --samples HOT 1
- ValueError: could not convert string to float
- bug found? HOT 1
- what the columns when the inputs are bed files? HOT 1
- Can I use IDR to analyze ChIPseq or Cuttag data of histones?
- IDR with small number of peaks
- Error running with bed file
- ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() HOT 5
- idr excludes top peaks HOT 1
- idr --samples peak1 peak2 : Number of peaks passing IDR cutoff of 0.05 - 0/50537 (0.0%) HOT 1
- error: Use a.any() or a.all()_ HOT 3
- pkg_resources.DistributionNotFound
- Parameter requirements for input file in BED format?
- installation issues
- IDR-pooled peak list
- idr:idr has no attribute 'fit_model_and_calc_local_idr'
- Irreproducible Discovery Rate (IDR) for 3 replicates HOT 3
- AttributeError: module 'numpy' has no attribute 'int' HOT 2
- --input-file-type bed expecting 9 columns HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from idr.