izhbannikov / haplor Goto Github PK

Hi,

I've been having some issues with Haplogrep when using a vcf file. I run --format vcf so haplogrep is aware but the quality of the haplogroup assignment is between 50-70%.

When I convert the file to the hsd file format that Haplogrep required originally, haplogrep runs beautifully with 95% of individuals receiving a quality score of >90%.

I was just wondering if anyone had encountered a similar issue? Is there an extra step one needs to perform when working with a .vcf file?

Thank you in advance!

Dear izhbannikov

The regulomeDB release a new website beta version. the current "queryRegulome()" command fail to accsse to the url(http://www.regulomedb.org/results). could you help us to solve it.

appreciate your help. Thanks.

Handle errors such as:
"Error in curl::curl_fetch_memory(url, handle = handle) :
Transferred a partial file"

Hi,
I am getting following error while using haploR package. How can I solve it?

URL does not seem to exist: https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php Here's the original error message: Timeout was reached: Operation timed out after 100003 milliseconds with 16378218 bytes received

I will appreciate your help. Thanks.

Hi

Thanks for developing such a nice package!

After querying HaploReg, and having obtained the names of the regulatory motifs, is there a way from within R to quickly generate the sequence logos for those regulatory motifs, from their names?

If one snp was not found in regulomedb it will output html content even if all other submitted snps are good. Need to fix it somehow.

Hi!

I noticed that since two weeks ago, haploR (v4.0.5) returns the error in the issue title: tmp.tables[[i]]: subscript out of bounds.

I have re-installed haploR as you suggest in the github and all the dependencies seem OK, so I have no idea what might be wrong. Would you mind checking this out?

Let me know if you can replicate the error. If not, I will share the rest of the info of my R session.

Thanks for looking into it in advance. I am at your disposition to help :)

Cheers,

Mario

For example, split it somehow.