mixcr analyze shotgun and exports?

[bbimber]

hello - we are running analyze shotgun w/ MiXCR 3. this pipeline appears to always run export; however, the results are not quite what I expect. it outputs separate text files for each of: ALL, IGH, IGK, IGL, TRA, TRB, TRD, and TRG. for example: prefix.clonotypes.ALL.txt. all of these files appear identical though. is this expected?

also, is it possible to suppress the export command?

[PoslavskySV]

Thanks for reporting!

all of these files appear identical though. is this expected?

this is a bug. Will be fixed at the end of the week.

also, is it possible to suppress the export command?

Unfortunately, not. I'll add this feature in the upcoming release (at the end of the week).

[bbimber]

great, thanks. the single command 'analyze' is a very useful new feature.

[PoslavskySV]

fixed via 29bd9ea

[AnaBolivar]

hello
I am having the same issue when running the analyze amplicon pipeline with mixcr 3.0.1 of 5'RACE cDNA libraries. It outputs 4 txt files (TRA, TRB, TRD and TRG) that appear to be identical. Is it possible that it is the same bug?

[dbolotin]

This was fixed in 3.0.3, please use latest MiXCR version, which is currently 3.0.10.

[AnaBolivar]

Hi Dmitry Thank you for your quick response, I have done so and now it is giving me different files for TRA and TRB, but TRD is the same as the TRA file and the TRG file is empty. What is the difference between the single clones.txt file, generated using the default command *exportClones* outside of the *analyze amplicon* pipeline, and the four .txt files generated with *analyze amplicon*? Does the single file generated with the default exportClones command include all the sequences of TRA, TRB, TRD and TRG together in one file? I appreciate your help, Ana El vie., 27 de sep. de 2019 a la(s) 11:35, Dmitry Bolotin ( notifications@github.com) escribió:

…

This was fixed in 3.0.3, please use latest MiXCR version <https://github.com/milaboratory/mixcr/releases/latest>. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#454?email_source=notifications&email_token=ANKMQMYVIDWBDF4SADBJGGTQLYY35A5CNFSM4GDIKFTKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7ZOFNI#issuecomment-536011445>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ANKMQMYT6DC3PEKLUNOGFXLQLYY35ANCNFSM4GDIKFTA> .