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biocore-ntnu / epic

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
http://bioepic.readthedocs.io
MIT License
31 stars 6 forks source link

Effective genome size for Rnor6 #34

Closed abhisheksinghnl closed 8 years ago

abhisheksinghnl commented 8 years ago

Hi Could you please let me know, how I can numbers for effective genome size files in the for rat and pig?

And also for broad peaks like K9me2 what settings shall I use?

Thank you

endrebak commented 8 years ago

Thanks for your interest in epic :)

I have started computing the egs and chromsizes for

rn4 rn5 rn6 susScr3 susScr2

Since epic is so fast, you could try several and see which regions look best in a genome browser (without peeking at the p-values of course).

Since the standard settings are good for H3K27me3 they should work well for other broad modifications. I'll update epic tomorrow with the new genomes.

abhisheksinghnl commented 8 years ago

Thank you :)

On Thu, Aug 11, 2016 at 4:10 PM, Endre Bakken Stovner < notifications@github.com> wrote:

Thanks for your interest in epic :)

I have started computing the egs and chromsizes for

rn4 rn5 rn6 susScr3 susScr2

Since epic is so fast, you could try several and see which regions look best (without peeking at the p-values of course).

Since the standard settings are good for H3K27me3 they should work well for other broad modifications. I'll update epic tomorrow with the new genomes.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/endrebak/epic/issues/34#issuecomment-239172008, or mute the thread https://github.com/notifications/unsubscribe-auth/AUAA59t774ynk20j3XQdr2Q1w2jg2QQ_ks5qey09gaJpZM4JiJol .

abhisheksinghnl commented 8 years ago

Hi,

Please let me know after you have updated the genomes.

Thank you.

Best regards Abhishek

endrebak commented 8 years ago

There was maintenance on our servers yesterday so the script was ended while running. Restarted it now, might not be finished today. If not, I'll upload them on Monday.

endrebak commented 8 years ago

epic now includes rn4, rn5 and rn6. The pig genomes made my effective genome size script fail, which I will get around to fixing. Dunno when I'll succeed though, but I will be sure to reply here.

pip install bioepic==0.1.10

abhisheksinghnl commented 8 years ago

Thank you :)

Will wait for update on pig genome

On Fri, Aug 12, 2016 at 1:04 PM, Endre Bakken Stovner < notifications@github.com> wrote:

epic now includes rn4, rn5 and rn6. The pig genomes made my effective genome size script fail, which I will get around to fixing. Dunno when I'll succeed though, but I will be sure to reply here.

pip install bioepic==0.0.10

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/endrebak/epic/issues/34#issuecomment-239419622, or mute the thread https://github.com/notifications/unsubscribe-auth/AUAA58E2XQMI0PgdXtRh_4Rr_uETQyBtks5qfFNQgaJpZM4JiJol .

endrebak commented 8 years ago

0.1.11 is out and contains susScr3. I am done for the week, but I will add susScr2 eventually.

abhisheksinghnl commented 8 years ago

Thank you

On Fri, Aug 12, 2016 at 1:32 PM, Endre Bakken Stovner < notifications@github.com> wrote:

0.1.11 is out and contains susScr3. I am done for the week, but I will add susScr2 eventually.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/endrebak/epic/issues/34#issuecomment-239424101, or mute the thread https://github.com/notifications/unsubscribe-auth/AUAA542DbkB11RoSe5j051YgpTjl1Y2pks5qfFnogaJpZM4JiJol .

endrebak commented 8 years ago

susScr2 is in 0.1.13. You can now use upper- or lowercase to write the genome in any way you want now.

pip install bioepic=0.1.13.