TElocal index

[olivertam]

Dear Oliver Tam,

Thank you for providing very useful software. TEtranscripts and TElocal are the same, but, in order to run TElocal, we have to provide, indexed GTF files.

Could you show me some example how to generate this file, I do not have any ideas about this.

I can also use TEcount instead of TEtranscripts, and generate only count table alone that can be used for differential analysis.

the only difference is that TEtrnscripts will peroform differentiall analsis,

TElocal use indexed GTF file.

with regards

Ramky

Originally posted by @Ramkyeri in https://github.com/mhammell-laboratory/TEtranscripts/issues/33#issuecomment-987579062

[olivertam]

Hi

You can generate the pre-built index using the TE GTF that was previously created (the first one). As mentioned previously, you make the prebuilt index using the TElocal_indexer script (requires TElocal to be installed). The command line arguments are as follows:

$ TElocal_indexer --afile TE.gtf --itype TE

It is advisable to provide around 30Gb of RAM for index building. Like your previous TEtranscripts run, the index building will take a long time (~30 hours, if I recall correctly), but once completed, TElocal will just load the index for its run, which will substantially improve run-time.

Just a note: TElocal functions similarly to TEcount, in that it would not perform the differential analysis, but generate the count tables that you can then combine into a single count table to run your differential analysis. Please also note that TEtranscripts requires DESeq2 installed in order to perform differential analysis.

Please let us know if you have other questions.

Thanks

[Ramkyeri]

Dear Oliver Tam,

Thank you so much for your time and for showing me an example.

Yes, you are correct, it 30 hours to build an index. Thank you for remembering.

with regards

Ramky

[Ramkyeri]

Dear Oliver Tam,

while running the TElocal_indexer --afile TE.gtf --itype TE , it got the error, I have also installed TElocal .

with regards

Ramky

[olivertam]

Hi Ramky,

You will need to first make the script an executable:

$ chmod a+x TElocal_indexer

You can then run it from the directory where the script is located:

$ ./TElocal_indexer --afile TE.gtf --itype TE

Or copy the script to a folder containing your other binaries/executabes (e.g. where you TElocal is installed). This will then allow you run it from anywhere on your system

$ TElocal_indexer --afile TE.gtf --itype TE

Thanks.

[Ramkyeri]

Dear Oliver Tam,

Thank you for sharing the script.

with regards

Ramky

[Ramkyeri]

Dear Oliver Tam,

I do not why it still shows the error, I executed the file, using py extension.

With regards

Ramky

[Ramkyeri]

Dear Oliver Tam,

I think it is correct, I used this ./TElocal_indexer.py --afile TE.gtf --itype TE (.py)

with regards

Ramky

[olivertam]

Hi Ramky,

Yes, it appears the script was saved with the .py extension, and thus your solution is correct.

Thanks

[Ramkyeri]

Dear Oliver Tam,

Thank you for confirming this.

with regards Ramky

[Ramkyeri]

Dear Oliver Tam,

this is just for the update, TE indexing is completed, it took more than 50 hours. The output also says that this can be used only in TElocal.

TElocal do not require whether it is a control sample or treatment sample,

Can we run multiple BAM files, it shows error to me.

with regards

[olivertam]

Hi Ramky,

As previously mentioned, TElocal operates like TEcount, and takes only one sample at a time (agnostic to whether treatment or control). You will need to combine the outputs of various TElocal runs to perform your own differential analysis.

Thanks.

[Ramkyeri]

Dear Oliver Tam,

many thanks for your reply.

with regards

Ramky

[Ramkyeri]

Dear Oliver Tam,

Greetings! I would like to update the analysis. I used TE2.gtf fod indexing. it did not break the program in both TElocal_indexer.py and TElocal. with regards Ramky

[olivertam]

Thank you for the update.

[PinpinSui]

Hi Oliver Tam,

I install TElocal with the commond pip install TElocal in conda env. Would you like to tell me where can I find TElocal_indexer? Thank you,

Pinpin

[olivertam]

Hi Pinpin,

The TElocal_indexer is still in beta, hence we didn't include with TElocal. You can obtain it here

Thanks.

[ChiaraGTH]

Hi Oliver Tam, would it be possible to have a library where the .locInd files, of the various species, can be downloaded directly? The ones that are there are not up to date, and building index files takes a long time. Thanks.

[olivertam]

Hi,

Thank you for your interest in the software Currently, the .locInd index has to be built separately for each genome version. If you have a list of genomes that you would like us to build, let us know and we can try to help.

Thanks.

[pabisk]

Could you add a progress indicator to the indexing script? Since it can take multiple days to run it would be good to know whether it is working or getting stuck and how much time is left until it finishes.

[olivertam]

Hi,

We are currently in the process of improving the TElocal software to significantly speed up the TE index building process, and thus we are envisioning that the current indexing script will be deprecated. Therefore, we have no current plans to update the indexing script.

Thanks.

[watamine]

Dear Oliver Tam,

Thank you for your software. I installed TElocal and used TElocal_indexer. I started 7/20 but now 7/25 building index doesn't finish.

Why is it happened ? I used TEtranscripts index file for --afile TE.gtf

I would greatly appreciate it if you could let me know

watamine

[olivertam]

Hi watamine,

Thank you for your interest in the software. Depending on the size of the TE GTF file, it can take quite a while to build that index (days). If it is still not done after a week, please let us know and we can try to troubleshoot.

Apologies.

[watamine]

Hi Oliver Tam,

I see, Thank you.　I am going to wait for it.

I will contact you if anything happens

Thanks.

[watamine]

Hi Oliver Tam,

TElocal_indexer finished ! Thank you for your advice.

Thanks.