Missing access hg38 bed file

[ashwini06]

Hi,

I am looking for hg38 accessible bed file (access-5k-mappable.hg38.bed) in https://github.com/etal/cnvkit/tree/master/data and is missing. Can you please update it for downloading from data/ or instruct me for generate this file ?

Thank you!

[yulijia]

Hi, You could use cnvkit.py access command to generate any sequence-accessible coordinates file by yourself. Please see this page https://cnvkit.readthedocs.io/en/stable/pipeline.html#access

Calculate the sequence-accessible coordinates in chromosomes from the given reference genome, output as a BED file.

cnvkit.py access hg19.fa -x excludes.bed -o access-excludes.hg19.bed
cnvkit.py access mm10.fasta -s 10000 -o access-10kb.mm10.bed

[stroke1989]

@yulijia Hi, to generate sequence-accessible coordinates file, a file of regions of poor mappability is needed. Where I can get this file for hg38? Hope your response!

[awast]

Hello Sir stroke1989 If you have any update regarding generation of this file please share....

[yulijia]

@stroke1989 @awast

Please see this post to find the the mappability file https://www.biostars.org/p/487547/

[awast]

@stroke1989 @awast

Please see this post to find the the mappability file https://www.biostars.org/p/487547/

Thankyou Sir..