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mhammell-laboratory / TElocal

A package for quantifying transposable elements at a locus level for RNAseq datasets.
GNU General Public License v3.0
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Can I apply TElocal to Single End Sequencing #37

Open smarhon opened 2 months ago

smarhon commented 2 months ago

Hi

Can I apply TElocal to single end sequencing?

Thanks

olivertam commented 2 months ago

Hi,

Thank you for your interest in the software. Yes, you can use TElocal with single end libraries.

Thanks.

smarhon commented 2 months ago

Hi,

Thank you for your interest in the software. Yes, you can use TElocal with single end libraries.

Thanks.

Thank you so much.

Is there a tool that I can use to create my own index to use with TElocal tool? Or can I send you a GTF file and you create it form me?

Best Sajid

olivertam commented 2 months ago

Hi,

The TElocal_indexer is available. It is in beta, and may be deprecated in a future version of TElocal, but could be used now. Please note that it will take quite a while to generate the index if your TE annotation is large.

Thanks.

smarhon commented 2 months ago

Hi,

The TElocal_indexer is available. It is in beta, and may be deprecated in a future version of TElocal, but could be used now. Please note that it will take quite a while to generate the index if your TE annotation is large.

Thanks.

In this indexing tool, I have to select either gene or TE, but in your prebuilt index, you combine both of them in one index. If I need to combine both of them what should be the selection?

olivertam commented 2 months ago

Hi,

Our pre-built indices are for the TE, not the gene. You can also pre-built the gene index with the tool, but it's not required by TElocal. Thanks.

Cheers, Oliver

smarhon commented 2 months ago

Hi,

Our pre-built indices are for the TE, not the gene. You can also pre-built the gene index with the tool, but it's not required by TElocal. Thanks.

Cheers, Oliver

Thank you for your prompt response!

When I use your prebuilt index, it quantifies reads for genes and TEs. https://labshare.cshl.edu/shares/mhammelllab/www-data/TElocal/prebuilt_indices/hg38_rmsk_TE.gtf.locInd.gz

Am I am using the correct index?

Best Sajid

olivertam commented 2 months ago

Hi,

Could you provide the command line? You have to provide both a gene GTF (--GTF) and a TE index (--TE), so you will quantify both genes and TEs. It is actually crucial to quantify both at the same time, as "overlaps" between the two annotation sets are resolved differently depending on whether the read is uniquely or ambiguously mapped.

Thanks.

smarhon commented 2 months ago

Hi,

Could you provide the command line? You have to provide both a gene GTF (--GTF) and a TE index (--TE), so you will quantify both genes and TEs. It is actually crucial to quantify both at the same time, as "overlaps" between the two annotation sets are resolved differently depending on whether the read is uniquely or ambiguously mapped.

Thanks.

Sorry about that. Yes, because I am using both --GTF and --TE options. I did not pay attention to this. Thank you for the clarification.