Mira Tcs Output Currently Not Available

Question

[diltsjeri]

Hi,

I'm trying to find coverage and %calls at every bp in my resulting sequencing data. I chose MIRA because of this wonderful TCS file which is suppose to provide all this information, but after running the assemblies my file states "TCS output currently not available, please contact author". I did a mapping assembly. I'm not sure if TCS can be done with mapping assemblies. Has anyone else had this problem? Am I missing an option?

Has anyone tried using caf2tcs to force convert the caf file to tcs? or maf2sam?

Thanks!

[Vikas Bansal]

I am sure someone can help if you can give details about the version of MIRA and the command you used.

[diltsjeri]

No problem. MIRA 3.4.x . Command-->

mira --project=test --job=mapping,genome,accurate,iontor -MI:sonfs=no -SB:lb=1:sbuip=1:bsn=reference IONTOR_SETTINGS -AS:mrpc=100 >test_log_assembly.txt

Answer 1

[Leonor Palmeira]

Your error message says:

TCS output currently not available, please contact author

Have you tried this? The mira_talk mailing list is very active, and Bastien is always available to provide help on MIRA. Also, are you using the latest MIRA version? This might be already fixed and available in the new version.

Answer 2

[diltsjeri]

Not to bring up an old topic but TCS is still not available. However, after doing some communication with Francisco Martins on the mira_talk mailing list (as suggested above), he suggested I use his script "CAF_to_TCS.py". Worked like a charm!

[Leonor Palmeira]

Thanks for the update!