Closed zuta-osa77 closed 8 years ago
Hi,
1) You should use parse.mixcr
in order to parse the MiXCR files. Yes, first you run exportClones, and after that you parse the output files to R with parse.mixcr
. I think you could just run mixcr exportClones clones.clns clones.txt
, i.e., without any parameters, to get the suitable for tcR output tables.
2) You just need to put all your clns files to the same folder, and after that run your_list = parse.folder(path_to_your_folder, "mixcr")
. Run ?parse.folder
for more info.
I hope this helps. If not please message me here or by email.
hey thanks Vadim
On Wed, Aug 10, 2016 at 1:08 PM, Vadim Nazarov notifications@github.com wrote:
Hi,
1) You should use parse.mixcr in order to parse the MiXCR files. Yes, first you run exportClones, and after that you parse the output files to R with parse.mixcr. I think you could just run mixcr exportClones clones.clns clones.txt, i.e., without any parameters, to get the suitable for tcR output tables.
2) You just need to put all your clns files to the same folder, and after that run your_list = parse.folder(path_to_your_folder, "mixcr"). Run ?parse.folder for more info.
I hope this helps.
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No problems, please let me know if it works for you or not, so I would be able to help you / close this issue.
Yes this worked out, thanks again for your help. I have another related question concerning filtering this imported dataset -- would you prefer in the interests of good organization that I open a new issue, ask you this in private, or just ask here?
Nice! Regarding another question - please, either open a new issue or send me an email, which way is more comfortable for you.
hi all,
I'm new to this: I've run mixcr/1.8.1 on my RNA-seq dataset using the partialAssemble workflow described on the main page and would like to create the analog of the
twa
list object in R which represents the Cloneset. I have several questions:1) I'm guessing I need to run exportClones with a couple of specified fields in order to use
parse.mitcr
directly on it. Is this correct? If so, would anybody have the exact call to exportClones which would allow the output to be directly input into a Cloneset object in R? I don't know in other words how
twa
ortwb
were generated or cherrypicked from exportClones output2) Along the same lines, how do I combine all the exportClones output from mixcr so that I can represent my entire dataset in a Cloneset, e.g. all four subjects are in
twa
Basically, if there was a concrete example of how to go from N clns files (from mixcr assemble) to N exportClones files with the right fields picked out to be directly input into tcR, and then make a N x 1 list containing the entire dataset in a Cloneset object, that would be great!
Looks like a great set of routines and visualization scripts, so I can't wait to use it.
all the best, zo