Cannot find Separate Bed files

MariaCartolano commented 1 month ago

Hello

thank you for this great resource!

After inspecting the data I noticed that I am better off downloading separate bed files, selected based on the sample origin. In fact, after having downloaded the assembled peaks, I noticed that the sample source is quite heterogeneous ( e.g. samples from healthy and diseased patients are assembled together) and it does not help me.

I have been selecting the original bed files of interest upon manual filtering of the experimentList file and I was going to download them from

http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/eachData/bed05/

however in this directory I cannot find the bed files I am looking for. Can you please help me?

This is the list of files I am interested in:

Thank you for your help Maria

shinyaoki commented 1 month ago

Hi Maria,

Thank you for using ChIP-Atlas. The URL you tested is old. The current URL is as follows: https://chip-atlas.dbcls.jp/data/hg19/eachData/bed05/SRX8083175.05.bed

See also the documentation page to learn more about the URLs. https://github.com/inutano/chip-atlas/wiki#9-downloads

Best, Shinya

OKI, Shinya, PhD, Professor IRDA (Institute of Resource Development and Analysis), Kumamoto University 606 GTC Bldg, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan tel: +81-96-373-6501 https://oki-lab.jp/en/

2024/09/25 17:36、MariaCartolano @.***>のメール:

Hello

thank you for this great resource!

After inspecting the data I noticed that I am better off downloading separate bed files, selected based on the sample origin. In fact, after having downloaded the assembled peaks, I noticed that the sample source is quite heterogeneous ( e.g. samples from healthy and diseased patients are assembled together) and it does not help me.

I have been selecting the original bed files of interest upon manual filtering of the experimentList file and I was going to download them from

http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/eachData/bed05/

however in this directory I cannot find the bed files I am looking for. Can you please help me?

This is the list of files I am interested in:

SRX8083175 | hg19 | ATAC-Seq | Blood | Naive B cells SRX8083176 | hg19 | ATAC-Seq | Blood | Naive B cells SRX8083177 | hg19 | ATAC-Seq | Blood | Naive B cells ERX9147763 | hg19 | ATAC-Seq | Blood | Memory B cells ERX9147764 | hg19 | ATAC-Seq | Blood | Memory B cells ERX9147766 | hg19 | ATAC-Seq | Blood | Memory B cells ERX9147767 | hg19 | ATAC-Seq | Blood | Memory B cells ERX9147769 | hg19 | ATAC-Seq | Blood | Memory B cells ERX9147770 | hg19 | ATAC-Seq | Blood | Memory B cells SRX11161005 | hg19 | H3K27me3 | Blood | Naive B cells SRX16495765 | hg19 | H3K27me3 | Blood | Naive B cells SRX16495766 | hg19 | H3K27me3 | Blood | Naive B cells SRX16500133 | hg19 | H3K27me3 | Blood | Naive B cells SRX16500134 | hg19 | H3K27me3 | Blood | Naive B cells SRX11159883 | hg19 | H3K9me3 | Blood | Memory B cells SRX11159884 | hg19 | H3K9me3 | Blood | Memory B cells SRX11167811 | hg19 | H3K9me3 | Blood | Memory B cells SRX11167812 | hg19 | H3K9me3 | Blood | Memory B cells

Thank you for your help Maria

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MariaCartolano commented 1 month ago

ohi! Thank you so much for the swift reply! I did not notice there were 2 different links. I found the old one in a closed issue . Sorry about that !

maria

inutano / chip-atlas

Cannot find Separate Bed files #140