GRCh39 ensemble

[songlyzz]

Dear Oliver Tam, Hi I would like to download GRCm39 from https://labshare.cshl.edu/shares/mhammelllab/www-data/TElocal/prebuilt_indices/?C=D;O=A ，but there is only gencode GRCm39, I am fraid that it is not match the ensemble GRCm39 gene GTF, could you please offer me the reference locInd file? THANK YOU !

[olivertam]

Hi,

Thank you for your interest in the software. We are now generating the GRCm39 Ensembl TE index, and will let you know once that this ready.

Thanks.

[songlyzz]

Hi，Oliver Tam That is very nice of you, and I have another question that I ran TEtranscripts and had the project.cntTable, it is ~ 1.17M but today when I run TElocal ,that the result file surprisely ~ 139M almost 100X than TEtranscripts. But when I open it I found it is the same format. Is it just OK?

[olivertam]

Hi,

The difference between TEtranscripts count table and TElocal count table is that each TE copy in the genome is now a separate entry in the latter, whereas they are all aggregated by subfamily in the former. Thus, instead of just one entry for IAPEz-int, there are now multiple entries for each IAPEz-int copy in the genome. If you want to do differential anallysis on this output, we do recommend that you might want to remove lines that are below a certain threshold. You can either remove all entries with zero counts in all libraries, or perhaps requiring an average of 1 read across all libraries, or whatever other threshold. This will remove TE copies that are not expressed, and thus reduce the impact of p-value multiple-testing correction (e.g. FDR).

Please let me know if you have other questions.

Thanks

[songlyzz]

Hi ，Oliver Tam I understand it ! Thank you very much!

[olivertam]

Hi,

The index for GRCm39 Ensembl is ready.

Thanks