danrer10 umap results?

[Malcolm Cook]

can these be made available?

I see link for 

• Zebra fish danRer10 genome mappability

on page Umap and Bismap: quantifying genome and methylome mappability (hoffmanlab.org)

but it is 404

It would be grand if available.

Thanks!

[Mehran Karimzadeh]

Hi Malcolm,

Our server doesn't allow directory look up.

I need to generate an index for these pages which I'm too busy to do now.

A temporary solution though:

The bigWig files are named as:

k100_danRer10.bigWig  k27_danRer10.bigWig  k500_danRer10.bigWig  k750_danRer10.bigWig

k250_danRer10.bigWig  k35_danRer10.bigWig  k50_danRer10.bigWig   k76_danRer10.bigWig

To download, you can try: https://bismap.hoffmanlab.org/raw/danrer10/k100_danRer10.bigWig

The uint files named as follows are under:

chr10.uint8.unique.gz  chr15.uint8.unique.gz  chr1.uint8.unique.gz   chr24.uint8.unique.gz  chr5.uint8.unique.gz  chrM.uint8.unique.gz
chr11.uint8.unique.gz  chr16.uint8.unique.gz  chr20.uint8.unique.gz  chr25.uint8.unique.gz  chr6.uint8.unique.gz
chr12.uint8.unique.gz  chr17.uint8.unique.gz  chr21.uint8.unique.gz  chr2.uint8.unique.gz   chr7.uint8.unique.gz
chr13.uint8.unique.gz  chr18.uint8.unique.gz  chr22.uint8.unique.gz  chr3.uint8.unique.gz   chr8.uint8.unique.gz
chr14.uint8.unique.gz  chr19.uint8.unique.gz  chr23.uint8.unique.gz  chr4.uint8.unique.gz   chr9.uint8.unique.gz

To download, you can visit: https://bismap.hoffmanlab.org/raw/uint/danrer10/umap/chr10.uint8.unique.gz

Hope this helps.

Best,

Mehran

On Mon, Jan 25, 2021 at 9:50 AM Malcolm Cook <malcol...@gmail.com> wrote:

That is great.  I hope to obtain the uint8 as well as the bed files.  Thank you so much.  I tried running it on our SGE but came up against run-time errors in calls to bowtie and hope not to have to debug those now with your help.... though eventually I may still wish to run umap myself from soup to nuts on other model organism genomes since my institute is working in quite a few and will soon hope to have so-called blacklist regions incorporating your mappability scores....

~ Malcolm Cook

On Sun, Jan 24, 2021 at 10:59 PM Mehran Karimzadeh <mehran.k...@gmail.com> wrote:

Hi Malcolm,

I don't know why the URLs have stopped working.

I'm no longer in Hoffman's lab but I forwarded your request to the lab's software developer.

Once this is resolved, I'll let you know.

Best,

Mehran

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