bismark [options] {-1 -2 | }
in bismark when i write this i get an error msg that
could not read file {-1
I dont know what is the problem with i. Although i have done with genome_preparation but dont know what to do with this step
Ahsan:
Hope this studies in RG can be helpful in answering your question.
Best regards,
Debra
https://www.researchgate.net/publicliterature.PublicLiterature.search.html?type=keyword&search-keyword=Bismark&search-abstract=&search=Search
Hey Ahsan,
A little off topic, but the lab recommend methylpy -- https://bitbucket.org/schultzmattd/methylpy/wiki/Vignettes. I used to use Bismark but switch over to this program. One perk of methylpy is it allows you to incorporate a non-conversion control -- like lambda DNA -- which is used downstream for a per site binomial test to call sites as methylated or un-methylated. This is built into the program. The output is very similar to Bismark, so any parsing scripts you have would be easily adaptable. There is also a differentially methylated finder (DMR) tool too. I hope this helps.
Adam
system(sprintf("file.rename (./tophat_out, ./tophat/%s)", d),intern = FALSE, ignore.stdout = FALSE, ignore.stderr = FALSE, wait = TRUE)
This command is giving me rror all the time.and i have to run this on a bulk of data.
sh: 1: Syntax error: word unexpected (expecting ")")
I dont knw wat to do
I would definitely recommend BS-Seeker2 (http://pellegrini.mcdb.ucla.edu/BS_Seeker2/)
http://pellegrini.mcdb.ucla.edu/BS_Seeker2/
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