Using --rank option no output about idr HOT 8 CLOSED

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 --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]

---

—
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 --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]

---

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.