New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
duplicate 'row.names' are not allowed #56
Comments
Hi Haochen,
Thank you for your email. hicrep is originally designed to evaluate
intra-chromosome reproducibility, for one chromosome at a time. But you
bring out a good point. We are recently working on speed up the pipeline,
as well as taking whole genome data and multiple file types. Please come
back to check my github page in a week or so. We will release a new version
shortly. Thank you.
Tao
…On Sat, Jun 3, 2017 at 11:45 AM, Haochen Li ***@***.***> wrote:
Hi,
I prepared whole genome Hi-C matrices to run hicrep. However, I got the
error as in the title. It seems that hicrep is trying to use the bin
position as rownames when processing the data and encounters rowname
duplicates when there are multiple chromosomes. So, does hicrep support
genome-wide Hi-C matrix? If there is any other specification of the input
matrix format, please let me know.
Thanks,
Haochen
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
<#56>, or mute the thread
<https://github.com/notifications/unsubscribe-auth/ATEu6_UGgWJqumGVt-EoW9OobBkrLb87ks5sAX-lgaJpZM4NvHo6>
.
--
Tao Yang
PhD Candidate
Bioinformatics and Genomics
Penn State University
|
Hi Haochen,
What is the format of genome-wide Hi-C data?
Tao
What is
On Sat, Jun 3, 2017 at 11:45 AM Haochen Li ***@***.***> wrote:
Hi,
I prepared whole genome Hi-C matrices to run hicrep. However, I got the
error as in the title. It seems that hicrep is trying to use the bin
position as rownames when processing the data and encounters rowname
duplicates when there are multiple chromosomes. So, does hicrep support
genome-wide Hi-C matrix? If there is any other specification of the input
matrix format, please let me know.
Thanks,
Haochen
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
<#56>, or mute the thread
<https://github.com/notifications/unsubscribe-auth/ATEu6_UGgWJqumGVt-EoW9OobBkrLb87ks5sAX-lgaJpZM4NvHo6>
.
--
Tao Yang
PhD Candidate
Bioinformatics and Genomics
Penn State University
|
Same as what's on the online tutorial. The N * (N + 3) matrix. I wrote
script to generate a text file in such format and load it into R as a
data.frame.
…On Sat, Jun 3, 2017 at 12:49 PM Tao Yang ***@***.***> wrote:
Hi Haochen,
What is the format of genome-wide Hi-C data?
Tao
What is
On Sat, Jun 3, 2017 at 11:45 AM Haochen Li ***@***.***>
wrote:
> Hi,
>
> I prepared whole genome Hi-C matrices to run hicrep. However, I got the
> error as in the title. It seems that hicrep is trying to use the bin
> position as rownames when processing the data and encounters rowname
> duplicates when there are multiple chromosomes. So, does hicrep support
> genome-wide Hi-C matrix? If there is any other specification of the input
> matrix format, please let me know.
>
> Thanks,
> Haochen
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <#56>, or mute the thread
> <
https://github.com/notifications/unsubscribe-auth/ATEu6_UGgWJqumGVt-EoW9OobBkrLb87ks5sAX-lgaJpZM4NvHo6
>
> .
>
--
Tao Yang
PhD Candidate
Bioinformatics and Genomics
Penn State University
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#56 (comment)>, or mute
the thread
<https://github.com/notifications/unsubscribe-auth/AOOjUge2boKi82-UZVlizHK7S8qtA1fCks5sAbjigaJpZM4NvHo6>
.
|
We internally store genome-wide matrix in hdf5 format (similar as what
cooler does). But I don't think hicrep supports that.
Haochen
…On Sat, Jun 3, 2017 at 12:49 PM Tao Yang ***@***.***> wrote:
Hi Haochen,
What is the format of genome-wide Hi-C data?
Tao
What is
On Sat, Jun 3, 2017 at 11:45 AM Haochen Li ***@***.***>
wrote:
> Hi,
>
> I prepared whole genome Hi-C matrices to run hicrep. However, I got the
> error as in the title. It seems that hicrep is trying to use the bin
> position as rownames when processing the data and encounters rowname
> duplicates when there are multiple chromosomes. So, does hicrep support
> genome-wide Hi-C matrix? If there is any other specification of the input
> matrix format, please let me know.
>
> Thanks,
> Haochen
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <#56>, or mute the thread
> <
https://github.com/notifications/unsubscribe-auth/ATEu6_UGgWJqumGVt-EoW9OobBkrLb87ks5sAX-lgaJpZM4NvHo6
>
> .
>
--
Tao Yang
PhD Candidate
Bioinformatics and Genomics
Penn State University
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#56 (comment)>, or mute
the thread
<https://github.com/notifications/unsubscribe-auth/AOOjUge2boKi82-UZVlizHK7S8qtA1fCks5sAbjigaJpZM4NvHo6>
.
|
The new version is compatible with cooler format. Release soon.
…On Sat, Jun 3, 2017 at 6:59 PM Haochen Li ***@***.***> wrote:
We internally store genome-wide matrix in hdf5 format (similar as what
cooler does). But I don't think hicrep supports that.
Haochen
On Sat, Jun 3, 2017 at 12:49 PM Tao Yang ***@***.***> wrote:
> Hi Haochen,
>
> What is the format of genome-wide Hi-C data?
>
> Tao
>
> What is
>
> On Sat, Jun 3, 2017 at 11:45 AM Haochen Li ***@***.***>
> wrote:
>
> > Hi,
> >
> > I prepared whole genome Hi-C matrices to run hicrep. However, I got the
> > error as in the title. It seems that hicrep is trying to use the bin
> > position as rownames when processing the data and encounters rowname
> > duplicates when there are multiple chromosomes. So, does hicrep support
> > genome-wide Hi-C matrix? If there is any other specification of the
input
> > matrix format, please let me know.
> >
> > Thanks,
> > Haochen
> >
> > —
> > You are receiving this because you are subscribed to this thread.
> > Reply to this email directly, view it on GitHub
> > <#56>, or mute the thread
> > <
>
https://github.com/notifications/unsubscribe-auth/ATEu6_UGgWJqumGVt-EoW9OobBkrLb87ks5sAX-lgaJpZM4NvHo6
> >
> > .
> >
> --
> Tao Yang
> PhD Candidate
> Bioinformatics and Genomics
> Penn State University
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <#56 (comment)>,
or mute
> the thread
> <
https://github.com/notifications/unsubscribe-auth/AOOjUge2boKi82-UZVlizHK7S8qtA1fCks5sAbjigaJpZM4NvHo6
>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<#56 (comment)>, or mute
the thread
<https://github.com/notifications/unsubscribe-auth/ATEu61JQd95YE_NvWZRDL3zKuFYaNXtlks5sAeU7gaJpZM4NvHo6>
.
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Hi,
I prepared whole genome Hi-C matrices to run hicrep. However, I got the error as in the title. It seems that hicrep is trying to use the bin position as rownames when processing the data and encounters rowname duplicates when there are multiple chromosomes. So, does hicrep support genome-wide Hi-C matrix? If there is any other specification of the input matrix format, please let me know.
Thanks,
Haochen
The text was updated successfully, but these errors were encountered: