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wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression
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explaining TE output #66

Open mars188 opened 2 years ago

mars188 commented 2 years ago

Hello,

I have outputted a file called "DESeq_TE_only.txt" and it looks fine but I am confused about the gene/TE names in the first column. For example, they look like this:

chr22|36735837|36736195|HE2_DR:tRNA-V:SINE|42|+,. chr1|25168232|25169679|TZF28B:TcMar-Tc1:DNA|78|-,. chr7|56584065|56584886|ERV1-N4-LTR_DR:LTR:LTR|17|+,. chr21|22685323|22686081|L2-34_DR:L2:LINE|128|-,.

I think actual TE name is "HE2_DR:tRNA-V:SINE". Is there any script to separate LINE, SINE, DNA and LTR classes of TEs?

mars188 commented 2 years ago

Also, I get TE and gens both mixed with each other in a single file. Is that normal?

There are two files of interest but I am confused what's the difference between them:

DESeq2_all: It contains genes and TE together DESeq2_TE_only: I thought it should contain only TEs but actually I see genes and TE together in this file.

Can you please help me understand the output results?

Many thanks,

Surar commented 2 years ago

Hi @mars188 have you found a way to separate LINE, SINE, DNA and LTR classes of TEs? Thanks.

mars188 commented 2 years ago

@Surar yes I did. I restarted with a freshly installed squire in a new/clean environment, and that solved the issues.

Surar commented 2 years ago

thanks, @mars188 will try so.