WARNING for calculating Pearson's and eigenvector at high resolution

[aidenlab]

WARNING for calculating Pearson's and eigenvector at high resolution

[nchernia]

Hi Tracy, Yes; be sure you're running the latest version of the Juicer tools: https://github.com/theaidenlab/juicer/wiki/Download You said it fails, how exactly? This is a warning but should continue to execute. https://github.com/theaidenlab/juicer/wiki/Eigenvector Best Neva

…

On Wed, Mar 15, 2017 at 1:04 PM, Tracy Ballinger ***@***.***> wrote: I'm calculating eigenvectors from hic files and when I go below 500,000 bp resolution, I get this warning: WARNING: Pearson's and eigenvector calculation at high resolution can take a long time and then it fails. It is possible to bypass this warning and forge ahead with higher resolution? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#10>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABWiW-hNCF7KCdKrnB4FEEZm98W2LO35ks5rl9PKgaJpZM4Md2cD> .

-- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

[TracyBallinger]

Hi Neva, I'm using the latest juicer for linux: juicer_tools_linux_0.8.jar. It doesn't give any error message other than the WARNING message, and it the exit status is 0, but the output file is empty.

…

On Wed, Mar 15, 2017 at 12:09 PM, nchernia ***@***.***> wrote: Hi Tracy, Yes; be sure you're running the latest version of the Juicer tools: https://github.com/theaidenlab/juicer/wiki/Download You said it fails, how exactly? This is a warning but should continue to execute. https://github.com/theaidenlab/juicer/wiki/Eigenvector Best Neva On Wed, Mar 15, 2017 at 1:04 PM, Tracy Ballinger ***@***.*** > wrote: > I'm calculating eigenvectors from hic files and when I go below 500,000 bp > resolution, I get this warning: > WARNING: Pearson's and eigenvector calculation at high resolution can take > a long time > and then it fails. > > It is possible to bypass this warning and forge ahead with higher > resolution? > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#10>, or mute the thread > <https://github.com/notifications/unsubscribe-auth/ABWiW- hNCF7KCdKrnB4FEEZm98W2LO35ks5rl9PKgaJpZM4Md2cD> > . > -- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGaYEPcOeTMkSaKP-fLF17KbN7QzZkWaks5rl9UQgaJpZM4Md2cD> .

[nchernia]

Are you using normalization? What happens when you dump the normalization vector? On Wed, Mar 15, 2017 at 1:22 PM, Tracy Ballinger <[email protected]> wrote:

…

Hi Neva, I'm using the latest juicer for linux: juicer_tools_linux_0.8.jar. It doesn't give any error message other than the WARNING message, and it the exit status is 0, but the output file is empty. On Wed, Mar 15, 2017 at 12:09 PM, nchernia ***@***.***> wrote: > Hi Tracy, > > Yes; be sure you're running the latest version of the Juicer tools: > https://github.com/theaidenlab/juicer/wiki/Download > > You said it fails, how exactly? This is a warning but should continue to > execute. > > https://github.com/theaidenlab/juicer/wiki/Eigenvector > > Best > Neva > > On Wed, Mar 15, 2017 at 1:04 PM, Tracy Ballinger < ***@***.*** > > > wrote: > > > I'm calculating eigenvectors from hic files and when I go below 500,000 > bp > > resolution, I get this warning: > > WARNING: Pearson's and eigenvector calculation at high resolution can > take > > a long time > > and then it fails. > > > > It is possible to bypass this warning and forge ahead with higher > > resolution? > > > > — > > You are receiving this because you are subscribed to this thread. > > Reply to this email directly, view it on GitHub > > <#10>, or mute the thread > > <https://github.com/notifications/unsubscribe-auth/ABWiW- > hNCF7KCdKrnB4FEEZm98W2LO35ks5rl9PKgaJpZM4Md2cD> > > . > > > > > > -- > Neva Cherniavsky Durand, Ph.D. > Staff Scientist, Aiden Lab > www.aidenlab.org > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#10 (comment) >, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AGaYEPcOeTMkSaKP- fLF17KbN7QzZkWaks5rl9UQgaJpZM4Md2cD> > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABWiWy8E12eyEijXlr7UF6HB0KldMB_fks5rl9fwgaJpZM4Md2cD> .

-- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

[TracyBallinger]

When I "dump norm" it seems to work. juicer_tools_linux_0.8.jar dump norm KR $hicfile 2 BP 50000 testout head testout chr1 0 50000 0.02172486731905749 chr1 50000 100000 0.053103909518366355 chr1 100000 150000 0.05473967322479318 chr1 150000 200000 0.019763252510339318 chr1 200000 250000 0.09499512426279362 chr1 250000 300000 0.024859504758668157 chr1 300000 350000 NaN chr1 350000 400000 NaN chr1 400000 450000 NaN chr1 450000 500000 NaN

…

On Wed, Mar 15, 2017 at 12:27 PM, nchernia ***@***.***> wrote: Are you using normalization? What happens when you dump the normalization vector? On Wed, Mar 15, 2017 at 1:22 PM, Tracy Ballinger ***@***.*** > wrote: > Hi Neva, > I'm using the latest juicer for linux: juicer_tools_linux_0.8.jar. > > It doesn't give any error message other than the WARNING message, and it > the exit status is 0, but the output file is empty. > > On Wed, Mar 15, 2017 at 12:09 PM, nchernia ***@***.***> > wrote: > > > Hi Tracy, > > > > Yes; be sure you're running the latest version of the Juicer tools: > > https://github.com/theaidenlab/juicer/wiki/Download > > > > You said it fails, how exactly? This is a warning but should continue to > > execute. > > > > https://github.com/theaidenlab/juicer/wiki/Eigenvector > > > > Best > > Neva > > > > On Wed, Mar 15, 2017 at 1:04 PM, Tracy Ballinger < > ***@***.*** > > > > > wrote: > > > > > I'm calculating eigenvectors from hic files and when I go below 500,000 > > bp > > > resolution, I get this warning: > > > WARNING: Pearson's and eigenvector calculation at high resolution can > > take > > > a long time > > > and then it fails. > > > > > > It is possible to bypass this warning and forge ahead with higher > > > resolution? > > > > > > — > > > You are receiving this because you are subscribed to this thread. > > > Reply to this email directly, view it on GitHub > > > <#10>, or mute the thread > > > <https://github.com/notifications/unsubscribe-auth/ABWiW- > > hNCF7KCdKrnB4FEEZm98W2LO35ks5rl9PKgaJpZM4Md2cD> > > > . > > > > > > > > > > > -- > > Neva Cherniavsky Durand, Ph.D. > > Staff Scientist, Aiden Lab > > www.aidenlab.org > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub > > <#10 issuecomment-286723200 > >, > > or mute the thread > > <https://github.com/notifications/unsubscribe-auth/AGaYEPcOeTMkSaKP- > fLF17KbN7QzZkWaks5rl9UQgaJpZM4Md2cD> > > . > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#10 (comment) >, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ ABWiWy8E12eyEijXlr7UF6HB0KldMB_fks5rl9fwgaJpZM4Md2cD> > . > -- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGaYEC1ASD9hNyWYhuM9hDHOvdfkev_Vks5rl9lOgaJpZM4Md2cD> .

[nchernia]

Would you be willing to share the .hic file and I can test? I haven't seen this behavior before. If you are willing, send me your email and I'll invite you to a Box folder to deposit it. You can email me at [email protected] On Wed, Mar 15, 2017 at 2:24 PM, Tracy Ballinger <[email protected]> wrote:

…

When I "dump norm" it seems to work. juicer_tools_linux_0.8.jar dump norm KR $hicfile 2 BP 50000 testout head testout chr1 0 50000 0.02172486731905749 chr1 50000 100000 0.053103909518366355 chr1 100000 150000 0.05473967322479318 chr1 150000 200000 0.019763252510339318 chr1 200000 250000 0.09499512426279362 chr1 250000 300000 0.024859504758668157 chr1 300000 350000 NaN chr1 350000 400000 NaN chr1 400000 450000 NaN chr1 450000 500000 NaN On Wed, Mar 15, 2017 at 12:27 PM, nchernia ***@***.***> wrote: > Are you using normalization? What happens when you dump the normalization > vector? > > On Wed, Mar 15, 2017 at 1:22 PM, Tracy Ballinger < ***@***.*** > > > > wrote: > > > Hi Neva, > > I'm using the latest juicer for linux: juicer_tools_linux_0.8.jar. > > > > It doesn't give any error message other than the WARNING message, and it > > the exit status is 0, but the output file is empty. > > > > On Wed, Mar 15, 2017 at 12:09 PM, nchernia ***@***.***> > > wrote: > > > > > Hi Tracy, > > > > > > Yes; be sure you're running the latest version of the Juicer tools: > > > https://github.com/theaidenlab/juicer/wiki/Download > > > > > > You said it fails, how exactly? This is a warning but should continue > to > > > execute. > > > > > > https://github.com/theaidenlab/juicer/wiki/Eigenvector > > > > > > Best > > > Neva > > > > > > On Wed, Mar 15, 2017 at 1:04 PM, Tracy Ballinger < > > ***@***.*** > > > > > > > wrote: > > > > > > > I'm calculating eigenvectors from hic files and when I go below > 500,000 > > > bp > > > > resolution, I get this warning: > > > > WARNING: Pearson's and eigenvector calculation at high resolution can > > > take > > > > a long time > > > > and then it fails. > > > > > > > > It is possible to bypass this warning and forge ahead with higher > > > > resolution? > > > > > > > > — > > > > You are receiving this because you are subscribed to this thread. > > > > Reply to this email directly, view it on GitHub > > > > <#10>, or mute the > thread > > > > <https://github.com/notifications/unsubscribe-auth/ABWiW- > > > hNCF7KCdKrnB4FEEZm98W2LO35ks5rl9PKgaJpZM4Md2cD> > > > > . > > > > > > > > > > > > > > > > -- > > > Neva Cherniavsky Durand, Ph.D. > > > Staff Scientist, Aiden Lab > > > www.aidenlab.org > > > > > > — > > > You are receiving this because you authored the thread. > > > Reply to this email directly, view it on GitHub > > > <#10 > issuecomment-286723200 > > >, > > > or mute the thread > > > <https://github.com/notifications/unsubscribe-auth/AGaYEPcOeTMkSaKP- > > fLF17KbN7QzZkWaks5rl9UQgaJpZM4Md2cD> > > > . > > > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub > > <#10 issuecomment-286725720 > >, > > or mute the thread > > <https://github.com/notifications/unsubscribe-auth/ > ABWiWy8E12eyEijXlr7UF6HB0KldMB_fks5rl9fwgaJpZM4Md2cD> > > > . > > > > > > -- > Neva Cherniavsky Durand, Ph.D. > Staff Scientist, Aiden Lab > www.aidenlab.org > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#10 (comment) >, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ AGaYEC1ASD9hNyWYhuM9hDHOvdfkev_Vks5rl9lOgaJpZM4Md2cD> > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABWiW_vfHMvkYAS0Rt4YfDe233QT8RMpks5rl-ajgaJpZM4Md2cD> .

-- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

[TracyBallinger]

The hic file is just one from the RAO et al dataset: You can get it here: wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_GM12878_insitu_primary%2Breplicate_combined.hic.gz

…

On Wed, Mar 15, 2017 at 1:32 PM, nchernia ***@***.***> wrote: Would you be willing to share the .hic file and I can test? I haven't seen this behavior before. If you are willing, send me your email and I'll invite you to a Box folder to deposit it. You can email me at ***@***.*** On Wed, Mar 15, 2017 at 2:24 PM, Tracy Ballinger ***@***.*** > wrote: > When I "dump norm" it seems to work. > > juicer_tools_linux_0.8.jar dump norm KR $hicfile 2 BP 50000 testout > > head testout > > chr1 0 50000 0.02172486731905749 > > chr1 50000 100000 0.053103909518366355 > > chr1 100000 150000 0.05473967322479318 > > chr1 150000 200000 0.019763252510339318 > > chr1 200000 250000 0.09499512426279362 > > chr1 250000 300000 0.024859504758668157 > > chr1 300000 350000 NaN > > chr1 350000 400000 NaN > > chr1 400000 450000 NaN > > chr1 450000 500000 NaN > > On Wed, Mar 15, 2017 at 12:27 PM, nchernia ***@***.***> > wrote: > > > Are you using normalization? What happens when you dump the normalization > > vector? > > > > On Wed, Mar 15, 2017 at 1:22 PM, Tracy Ballinger < > ***@***.*** > > > > > > > wrote: > > > > > Hi Neva, > > > I'm using the latest juicer for linux: juicer_tools_linux_0.8.jar. > > > > > > It doesn't give any error message other than the WARNING message, and > it > > > the exit status is 0, but the output file is empty. > > > > > > On Wed, Mar 15, 2017 at 12:09 PM, nchernia ***@***.*** > > > > wrote: > > > > > > > Hi Tracy, > > > > > > > > Yes; be sure you're running the latest version of the Juicer tools: > > > > https://github.com/theaidenlab/juicer/wiki/Download > > > > > > > > You said it fails, how exactly? This is a warning but should continue > > to > > > > execute. > > > > > > > > https://github.com/theaidenlab/juicer/wiki/Eigenvector > > > > > > > > Best > > > > Neva > > > > > > > > On Wed, Mar 15, 2017 at 1:04 PM, Tracy Ballinger < > > > ***@***.*** > > > > > > > > > wrote: > > > > > > > > > I'm calculating eigenvectors from hic files and when I go below > > 500,000 > > > > bp > > > > > resolution, I get this warning: > > > > > WARNING: Pearson's and eigenvector calculation at high resolution > can > > > > take > > > > > a long time > > > > > and then it fails. > > > > > > > > > > It is possible to bypass this warning and forge ahead with higher > > > > > resolution? > > > > > > > > > > — > > > > > You are receiving this because you are subscribed to this thread. > > > > > Reply to this email directly, view it on GitHub > > > > > <#10>, or mute the > > thread > > > > > <https://github.com/notifications/unsubscribe-auth/ABWiW- > > > > hNCF7KCdKrnB4FEEZm98W2LO35ks5rl9PKgaJpZM4Md2cD> > > > > > . > > > > > > > > > > > > > > > > > > > > > -- > > > > Neva Cherniavsky Durand, Ph.D. > > > > Staff Scientist, Aiden Lab > > > > www.aidenlab.org > > > > > > > > — > > > > You are receiving this because you authored the thread. > > > > Reply to this email directly, view it on GitHub > > > > <#10 > > issuecomment-286723200 > > > >, > > > > or mute the thread > > > > <https://github.com/notifications/unsubscribe- auth/AGaYEPcOeTMkSaKP- > > > fLF17KbN7QzZkWaks5rl9UQgaJpZM4Md2cD> > > > > . > > > > > > > > > > — > > > You are receiving this because you commented. > > > Reply to this email directly, view it on GitHub > > > <#10 > issuecomment-286725720 > > >, > > > or mute the thread > > > <https://github.com/notifications/unsubscribe-auth/ > > ABWiWy8E12eyEijXlr7UF6HB0KldMB_fks5rl9fwgaJpZM4Md2cD> > > > > > . > > > > > > > > > > > -- > > Neva Cherniavsky Durand, Ph.D. > > Staff Scientist, Aiden Lab > > www.aidenlab.org > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub > > <#10 issuecomment-286726909 > >, > > or mute the thread > > <https://github.com/notifications/unsubscribe-auth/ > AGaYEC1ASD9hNyWYhuM9hDHOvdfkev_Vks5rl9lOgaJpZM4Md2cD> > > . > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#10 (comment) >, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ABWiW_ vfHMvkYAS0Rt4YfDe233QT8RMpks5rl-ajgaJpZM4Md2cD> > . > -- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGaYEA4w8W-D7nZS513cyXZgAuj6pk9kks5rl-hugaJpZM4Md2cD> .

[nchernia]

Hmm, sorry about that, we might need to think about the logic and either change it or update the documentation. Send in a "-p" flag to override. Note that you can access that file via URL (i.e. send in this URL instead of the filename): https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined.hic On Wed, Mar 15, 2017 at 2:47 PM, Tracy Ballinger <[email protected]> wrote:

…

The hic file is just one from the RAO et al dataset: You can get it here: wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/ suppl/GSE63525_GM12878_insitu_primary%2Breplicate_combined.hic.gz On Wed, Mar 15, 2017 at 1:32 PM, nchernia ***@***.***> wrote: > Would you be willing to share the .hic file and I can test? I haven't seen > this behavior before. > > If you are willing, send me your email and I'll invite you to a Box folder > to deposit it. You can email me at ***@***.*** > > On Wed, Mar 15, 2017 at 2:24 PM, Tracy Ballinger < ***@***.*** > > > > wrote: > > > When I "dump norm" it seems to work. > > > > juicer_tools_linux_0.8.jar dump norm KR $hicfile 2 BP 50000 testout > > > > head testout > > > > chr1 0 50000 0.02172486731905749 > > > > chr1 50000 100000 0.053103909518366355 > > > > chr1 100000 150000 0.05473967322479318 > > > > chr1 150000 200000 0.019763252510339318 > > > > chr1 200000 250000 0.09499512426279362 > > > > chr1 250000 300000 0.024859504758668157 > > > > chr1 300000 350000 NaN > > > > chr1 350000 400000 NaN > > > > chr1 400000 450000 NaN > > > > chr1 450000 500000 NaN > > > > On Wed, Mar 15, 2017 at 12:27 PM, nchernia ***@***.***> > > wrote: > > > > > Are you using normalization? What happens when you dump the > normalization > > > vector? > > > > > > On Wed, Mar 15, 2017 at 1:22 PM, Tracy Ballinger < > > ***@***.*** > > > > > > > > > > wrote: > > > > > > > Hi Neva, > > > > I'm using the latest juicer for linux: juicer_tools_linux_0.8.jar. > > > > > > > > It doesn't give any error message other than the WARNING message, and > > it > > > > the exit status is 0, but the output file is empty. > > > > > > > > On Wed, Mar 15, 2017 at 12:09 PM, nchernia < ***@***.*** > > > > > > wrote: > > > > > > > > > Hi Tracy, > > > > > > > > > > Yes; be sure you're running the latest version of the Juicer tools: > > > > > https://github.com/theaidenlab/juicer/wiki/Download > > > > > > > > > > You said it fails, how exactly? This is a warning but should > continue > > > to > > > > > execute. > > > > > > > > > > https://github.com/theaidenlab/juicer/wiki/Eigenvector > > > > > > > > > > Best > > > > > Neva > > > > > > > > > > On Wed, Mar 15, 2017 at 1:04 PM, Tracy Ballinger < > > > > ***@***.*** > > > > > > > > > > > wrote: > > > > > > > > > > > I'm calculating eigenvectors from hic files and when I go below > > > 500,000 > > > > > bp > > > > > > resolution, I get this warning: > > > > > > WARNING: Pearson's and eigenvector calculation at high resolution > > can > > > > > take > > > > > > a long time > > > > > > and then it fails. > > > > > > > > > > > > It is possible to bypass this warning and forge ahead with higher > > > > > > resolution? > > > > > > > > > > > > — > > > > > > You are receiving this because you are subscribed to this thread. > > > > > > Reply to this email directly, view it on GitHub > > > > > > <#10>, or mute the > > > thread > > > > > > <https://github.com/notifications/unsubscribe-auth/ABWiW- > > > > > hNCF7KCdKrnB4FEEZm98W2LO35ks5rl9PKgaJpZM4Md2cD> > > > > > > . > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Neva Cherniavsky Durand, Ph.D. > > > > > Staff Scientist, Aiden Lab > > > > > www.aidenlab.org > > > > > > > > > > — > > > > > You are receiving this because you authored the thread. > > > > > Reply to this email directly, view it on GitHub > > > > > <#10 > > > issuecomment-286723200 > > > > >, > > > > > or mute the thread > > > > > <https://github.com/notifications/unsubscribe- > auth/AGaYEPcOeTMkSaKP- > > > > fLF17KbN7QzZkWaks5rl9UQgaJpZM4Md2cD> > > > > > . > > > > > > > > > > > > > — > > > > You are receiving this because you commented. > > > > Reply to this email directly, view it on GitHub > > > > <#10 > > issuecomment-286725720 > > > >, > > > > or mute the thread > > > > <https://github.com/notifications/unsubscribe-auth/ > > > ABWiWy8E12eyEijXlr7UF6HB0KldMB_fks5rl9fwgaJpZM4Md2cD> > > > > > > > . > > > > > > > > > > > > > > > > -- > > > Neva Cherniavsky Durand, Ph.D. > > > Staff Scientist, Aiden Lab > > > www.aidenlab.org > > > > > > — > > > You are receiving this because you authored the thread. > > > Reply to this email directly, view it on GitHub > > > <#10 > issuecomment-286726909 > > >, > > > or mute the thread > > > <https://github.com/notifications/unsubscribe-auth/ > > AGaYEC1ASD9hNyWYhuM9hDHOvdfkev_Vks5rl9lOgaJpZM4Md2cD> > > > . > > > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub > > <#10 issuecomment-286739758 > >, > > or mute the thread > > <https://github.com/notifications/unsubscribe-auth/ABWiW_ > vfHMvkYAS0Rt4YfDe233QT8RMpks5rl-ajgaJpZM4Md2cD> > > > . > > > > > > -- > Neva Cherniavsky Durand, Ph.D. > Staff Scientist, Aiden Lab > www.aidenlab.org > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#10 (comment) >, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AGaYEA4w8W- D7nZS513cyXZgAuj6pk9kks5rl-hugaJpZM4Md2cD> > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABWiW7l0x07yvVxoNb2AsXSvh4UXZlEyks5rl-v8gaJpZM4Md2cD> .

-- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

[zeeev]

I had the same problem on another dataset. The -p does work, but seems like a bug.

[wjyzidane]

I have the same problem too. Is there a way to fix it now?

[nchernia]

Send in the -p flag to overrride.

On Thu, Feb 8, 2018 at 10:40 PM wjyzidane ***@***.***> wrote: I have the same problem too. Is there a way to fix it now? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABWiW-6Lh8O-ln5C5nanjLSff5AHZ5snks5tS74ugaJpZM4Md2cD> .

-- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

[shresthamit]

Hi,

I'm very new at this. We used Juicer to analyze our Hi-C data. Currently, we only have enough reads to generate maps at low resolution ( best around 250kb).

I was wondering if anyone could explain or direct me to the information regarding the eigenvector analysis. Just have a few simple questions

1. In the track which compartment is denoted in red and which in blue?
2. What is the default setting for compartment assignment as the sign is arbitrary?

Thank you very much,

Best regards,
Amit

[nchernia]

The sign is arbitrary and thus the red/blue is as well. You can correlate with activation marks to determine open compartment. Generally questions like these should be posted on the forum: aidenlab.org/forum.html

[nchernia]

The Pearson's / Eigenvector behavior should be fixed, but this is actually a Juicebox issue since the code base is in that repository. Moving over there.