Mandatory inputs
js8hh opened this issue · 3 comments
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
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.
Thanks Johnny for the helpful comment!
Natsuhiko
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