Mandatory inputs

[js8hh]

Hi,

Hope you are having a great day.

I had a question regarding the mandatory inputs for rasqual. In the documentaion, I found the followings as mandatory input for the rasqual package.

-y/--feature-counts File name of total feature counts in binary double
-k/--sample-offsets File name of sample specific offset terms in binary double
-s/--feature-starts Feature start position(s) in comma separated value (e.g., 100,300,500)
-e/--feature-ends Feature end position(s) in comma separated value (e.g., 150,350,450)
-j/--feature-id Row number of target feature in original count table
-l/--number-of-testing-snps Number of testing SNPs in VCF (candidates of a rSNP)
-m/--number-of-fsnps Number of feature SNPs (fSNPs) in VCF
-n/--sample-size Sample size

Among these, I wasn't sure how to get -s, -e, -l, and -m. I went through the page that explained how to get inputs for -y and -k, but wasn't sure about other ones.

I also found someone using rasqual with just -y, -k, and -x inputs, and was wondering if this is what I am supposed to do if I want to perform for all data, rather than few selected ones.

Thank you.

Best,
Joon Yuhl Soh

[iamjli]

Check out this fork and specifically the README in rasqualTools. There are lots of convenience functions for preparing your data. After running through the README, I split by batch then used run_Rasqual.pyto run. You won't need to specify any of these parameters explicitly if done correctly.

[natsuhiko]

Thanks Johnny for the helpful comment!
Natsuhiko

[js8hh]

Hi,

Thank you for giving me the link

I have been following the readme for the past week and could not resolve the createASVCF.sh section.

Do you know how long it would take approximately? I have been running it with 16 cores for more than a day and it still have not finished

Best,
Joon