Question: Mira Tcs Output Currently Not Available
1
gravatar for diltsjeri
6.0 years ago by
diltsjeri410
Chicago, IL
diltsjeri410 wrote:

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!

mira • 1.2k views
ADD COMMENTlink modified 11 days ago by Biostar ♦♦ 20 • written 6.0 years ago by diltsjeri410

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

ADD REPLYlink written 6.0 years ago by Vikas Bansal2.3k

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

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by diltsjeri410
2
gravatar for Leonor Palmeira
6.0 years ago by
Leonor Palmeira3.6k
Li├Ęge, Belgium
Leonor Palmeira3.6k wrote:

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.

ADD COMMENTlink written 6.0 years ago by Leonor Palmeira3.6k
1
gravatar for diltsjeri
5.4 years ago by
diltsjeri410
Chicago, IL
diltsjeri410 wrote:

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!

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by diltsjeri410

Thanks for the update!

ADD REPLYlink written 5.4 years ago by Leonor Palmeira3.6k
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