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Welcome to Umap and Bismap mailing list.

You can download the software from our bitbucket page and find more about the software here.
The Umap and Bismap trackhub can be automatically loaded by clicking here.

We are glad to know about any complications you might have with installation and use of our software.

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XR S, Eric Roberts2

3/17/25

Request for Bismap mappability bigWig files for T2T-CHM13v2.0

Hi Xinran, Currently the software is on minimal support due the the original author no longer with

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Request for Bismap mappability bigWig files for T2T-CHM13v2.0

Hi Xinran, Currently the software is on minimal support due the the original author no longer with

3/17/25

Mame seynabou Diop, Mehran Karimzadeh3

11/25/24

Hello, Thank you fo your answer. I think then I'm in the wrong track. I want the data that will

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Hello, Thank you fo your answer. I think then I'm in the wrong track. I want the data that will

11/25/24

Mehran Karimzadeh

6/24/24

Re: question on mappability gaps in mm10

Hi James, Gaps in the bed files mean that the region is not uniquely mappable with k-mers of length

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Re: question on mappability gaps in mm10

Hi James, Gaps in the bed files mean that the region is not uniquely mappable with k-mers of length

6/24/24

許靖, Eric Roberts3

6/13/24

Inquiry Regarding Umap and Bismap

I found the following links on the forum: https://bismap.hoffmanlab.org/raw/uint/hg38all/umap/

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Inquiry Regarding Umap and Bismap

I found the following links on the forum: https://bismap.hoffmanlab.org/raw/uint/hg38all/umap/

6/13/24

Adnan Hashim, Eric Roberts2

11/23/23

Sorry for the delay, those repositories no longer exist! The new repository exists on github here:

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Sorry for the delay, those repositories no longer exist! The new repository exists on github here:

11/23/23

Dailu Guan, Eric Roberts2

8/23/23

Request For the bovine genome

Hello, We are not planning on providing additional genomes outside of human and mouse (hg38, and mm10

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Request For the bovine genome

Hello, We are not planning on providing additional genomes outside of human and mouse (hg38, and mm10

8/23/23

Johannes Nicolaus Wibisana, Delva Leão2

4/19/23

Error running get_kmers.py

Hi Nico, This just means you attributed an array that was too long in the --array option. For making

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Error running get_kmers.py

Hi Nico, This just means you attributed an array that was too long in the --array option. For making

4/19/23

Johannes Nicolaus Wibisana

4/16/23

Running umap locally

Hi all, I have difficulties in running the program locally. I tried to write the codes in a way that

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Running umap locally

Hi all, I have difficulties in running the program locally. I tried to write the codes in a way that

4/16/23

3/16/23

Warning! No unique k-mers for k24

Dear Mehran, I manage to get ubismap for my Dasypus novemcinctus genome going! However, I'm

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Warning! No unique k-mers for k24

Dear Mehran, I manage to get ubismap for my Dasypus novemcinctus genome going! However, I'm

3/16/23

2/21/23

umap mappability for dasnov3.0

Hi all, Is it possible to ask for the mappability file for dasypus novemcinctus? Here is the genome I

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umap mappability for dasnov3.0

Hi all, Is it possible to ask for the mappability file for dasypus novemcinctus? Here is the genome I

2/21/23

Rotem, … Pooran Dewari4

11/14/22

getKmers.py generates empty *.gz files

Hi Katherine, Just wondering if you managed to make it work. I am facing the same problem; fails with

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getKmers.py generates empty *.gz files

Hi Katherine, Just wondering if you managed to make it work. I am facing the same problem; fails with

11/14/22

11/14/22

TypeError running the test data

Hello, I have been trying to set up umap but the test run gives me this error: File "get_kmers.

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TypeError running the test data

Hello, I have been trying to set up umap but the test run gives me this error: File "get_kmers.

11/14/22

John Ogata, Mehran Karimzadeh3

7/18/22

Original genome

Thank you! On Monday, July 18, 2022 at 8:27:22 AM UTC-7 mehran.k...@gmail.com wrote: Hi John, https:/

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Original genome

Thank you! On Monday, July 18, 2022 at 8:27:22 AM UTC-7 mehran.k...@gmail.com wrote: Hi John, https:/

7/18/22

John Ogata, Mehran Karimzadeh3

5/11/22

Awesome I look forward to it! Thanks so much. Best, Jonathan On Wednesday, May 11, 2022 at 10:10:24

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Awesome I look forward to it! Thanks so much. Best, Jonathan On Wednesday, May 11, 2022 at 10:10:24

5/11/22

Jingga Inlora, Mehran Karimzadeh2

4/1/22

meaning of regions not covered in UMAPM24

Hello Jingga, Yes; the Umap bed files contain genomic regions uniquely mappable by at least 1 k-mer (

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meaning of regions not covered in UMAPM24

Hello Jingga, Yes; the Umap bed files contain genomic regions uniquely mappable by at least 1 k-mer (

4/1/22

3/9/22

bitbucket page broken

Dear Mehran, I noticed you have updated the package. When I tried to reinstall it using hg, the link

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bitbucket page broken

Dear Mehran, I noticed you have updated the package. When I tried to reinstall it using hg, the link

3/9/22

Zhaozhe Hao, Mehran Karimzadeh3

3/8/22

Generating chrsize.tsv?

Thank you for the help, Mechran! On Sunday, March 6, 2022 at 11:29:16 PM UTC+8 mehran.k...@gmail.com

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Generating chrsize.tsv?

Thank you for the help, Mechran! On Sunday, March 6, 2022 at 11:29:16 PM UTC+8 mehran.k...@gmail.com

3/8/22

3/7/22

GRCm39/mm39 umap files and slurm examples

Hello, We have received a lot of requests for GRCm39/mm39 unique mappability files. I finally got

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GRCm39/mm39 umap files and slurm examples

Hello, We have received a lot of requests for GRCm39/mm39 unique mappability files. I finally got

3/7/22

Nicholas Rouse, … Mehran Karimzadeh3

3/2/22

Request for GRCm39 (mm39) umap files

Sure, will add this soon. On Wed, Mar 2, 2022 at 8:25 AM Hong Jiang <scila...@gmail.com>

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Request for GRCm39 (mm39) umap files

Sure, will add this soon. On Wed, Mar 2, 2022 at 8:25 AM Hong Jiang <scila...@gmail.com>

3/2/22

Nauman Javed, Mehran Karimzadeh2

2/15/22

rheMac10 and rn7 bed files

Dear Nauman, Unfortunately we only have uint files for rn6 and nothing for macaca: https://bismap.

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rheMac10 and rn7 bed files

Dear Nauman, Unfortunately we only have uint files for rn6 and nothing for macaca: https://bismap.

2/15/22

Nicholas Rouse, Mehran Karimzadeh3

11/16/21

Request For GRCh38 bed files

Much appreciated. Thank you for the quick response. Best, Nick On Tuesday, November 16, 2021 at 5:52:

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Request For GRCh38 bed files

Much appreciated. Thank you for the quick response. Best, Nick On Tuesday, November 16, 2021 at 5:52:

11/16/21

Mehran Karimzadeh

9/27/21

Re: request for umap of rn7

Hello Panjun, The software repository is at: https://github.com/hoffmangroup/umap Unfortunately I don

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Re: request for umap of rn7

Hello Panjun, The software repository is at: https://github.com/hoffmangroup/umap Unfortunately I don

9/27/21

sandaruwan ratnayake

6/28/21

Questions on UMAP

Hello, I installed umap in conda virtual environment with python 2.7 and tried to run the test script

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Questions on UMAP

Hello, I installed umap in conda virtual environment with python 2.7 and tried to run the test script

6/28/21

Mehran Karimzadeh

5/31/21

Re: umap Mappability for rn6

Hi Konstantin, Attached, I am sending you the rnor6 (rat genome) umap uint files from 75-mer and 150-

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Re: umap Mappability for rn6

Hi Konstantin, Attached, I am sending you the rnor6 (rat genome) umap uint files from 75-mer and 150-

5/31/21

Irina Zhegalova, … Mehran Karimzadeh6

4/26/21

error when accessing to Umap repository

Hello Maciej, Any command starting with "qsub" assumes there is an SGE scheduler. If you

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error when accessing to Umap repository

Hello Maciej, Any command starting with "qsub" assumes there is an SGE scheduler. If you

4/26/21

Rachel Rosenthal, Mehran Karimzadeh3

2/26/21

Hi Mehran, I had a quick question about the "Convert numeric vectors to BED and Wiggle"

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Hi Mehran, I had a quick question about the "Convert numeric vectors to BED and Wiggle"

2/26/21

Zac Chatterton, Mehran Karimzadeh3

1/28/21

Ubismap on hybrid hg38 and mm10 genomes

OK. Will give it a go. Thank you for the prompt reply. Best, Zac On Jan 28, 2021, at 9:54 PM, Mehran

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Ubismap on hybrid hg38 and mm10 genomes

OK. Will give it a go. Thank you for the prompt reply. Best, Zac On Jan 28, 2021, at 9:54 PM, Mehran

1/28/21

Malcolm Cook, Mehran Karimzadeh2

1/26/21

danrer10 umap results?

Hi Malcolm, Our server doesn't allow directory look up. I need to generate an index for these

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danrer10 umap results?

Hi Malcolm, Our server doesn't allow directory look up. I need to generate an index for these

1/26/21

Gilad Evrony, Mehran Karimzadeh2

10/22/20

CHM13_v1 mappability

So in summary umap uses job arrays. In SGE, job arrays are in this format qsub -q <queuename> -

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CHM13_v1 mappability

So in summary umap uses job arrays. In SGE, job arrays are in this format qsub -q <queuename> -

10/22/20

Mehran Karimzadeh

3/4/20

Umap v1.2 — 0-based BED files

Hi everyone, Roger Kramer brought to my attention that the Umap and Bismap files are not really BED

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Umap v1.2 — 0-based BED files

Hi everyone, Roger Kramer brought to my attention that the Umap and Bismap files are not really BED

3/4/20

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