Link question

[Yiyun317]

hi,I can't find your link about"http://rth.dk/resources/mirnasponge/data/snp_mart.gz "and" http://rth.dk/resources/mirnasponge/data/mkl.dat" in the PredcircRNA.py

[xypan1232]

Hi,

Can you go to https://rth.dk/resources/webcircrna/download:
Software
Download WebCircRNA
there should be snp_mart.gz.

Because those data maybe be removed by the server administrator, and now I left the group. Maybe you can retrain the model and save it as mkl.dat.

Could I ask you just want to use our tool for predicting your sequences? maybe you can use our updated webserver: https://rth.dk/resources/webcircrna/

[Yiyun317]

Thank you so much! But I still can't find the “snp_mart.gz” in the WebCircRNA file. Could you tell me the resource about it in other website? How can I get those data ?

[xypan1232]

Can you give me your mail and I can share snp_mart.gz with you via google drive. it is too big to upload it to github.

[Yiyun317]

Thanks for your help！Could you send to me the 'placental_phylop46way.tar.gz' (It’s also in the link about 'http://rth.dk/resources/mirnasponge/data/placental_phylop46way.tar.gz', but I can’t find it) and the 'snp_mart.gz' ? My email address is dengyiyun23@gmail.com. Looking forward to your reply！

[mstricker13]

Hi, can you also please share the data 'snp_mart.gz', 'placental_phylop46way.tar.gz' and 'mkl.dat' with me? My email address is m_stricker13@cs.uni-kl.de
Kind regards.

[SYChen123]

Hi, sir, could you pls share the data 'snp_mart.gz' and 'placental_phylop46way.tar.gz' with me? My email is siyuanchen11@gmail.com. Thank you very much!

Best regards.

[Qiqing-Fu]

Hi, sir, could you pls share the data 'snp_mart.gz' and 'placental_phylop46way.tar.gz' with me? My email is siyuanchen11@gmail.com.
Maybe, could you post these sources on yun source?
Thank you very much!^-^

[xypan1232]

Can you download snp_mart.gz from https://rth.dk/resources/webcircrna/downloads/WebCircRNA.tar, which may contains snp_mart.gz. In addition, maybe you can use the same way to extract conservation features, where original conservation files is from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/.

[Qiqing-Fu]

thank you for your kindness， however. I didn't find snp_mart.gz from the downloaded WebCircRNA.tar（ https://rth.dk/resources/webcircrna/downloads/WebCircRNA.tar）, AND I also didn't find placental_phylop46way.tar.gz. ?-?

[xypan1232]

for snp_mart.gz, you can use a new link http://www.csbio.sjtu.edu.cn/bioinf/PredcircRNA/snp_mart.gz
For other data, now my PC does not have them.

[Qiqing-Fu]

Thank you very much, and I really get snp_mart.gz. ^_^.
Then I download original conservation files from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/ , and I get placentalMammals.phyloP46way.bw form that website.
Is that true?
thank you for your kindness.

[xypan1232]

you can downlaod it for each chromosome of 24 from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/, but you need figure out how to extract the conservation scores given the coordinate.

[Qiqing-Fu]

Oh, thank you.
I think extracting the conservation scores in the condition of corrdinate is a little difficlut for me &-&, let me have a try.
Best regards

[Qiqing-Fu]

I don't know how to extract the conservation scores given the coordinate.
Now I download chr1.phyloP46way.placental.wigFix.gz which contains the scores, should I download all the scores for all chromosomes? Is there any exited script for the extraction.
maybe the previous email contained placental_phylop46way.tar.gz? -
Thank u again.

[Qiqing-Fu]

I adpot your scripts and extract placental_phylop46way.tar.gz, but it's doubtful to confirm the line structure showed in your file.
How could I get the phscore_dict?
Thank u so much.