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wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression
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SQuIRE_gene_TE_counttable - problem #77

Closed mars188 closed 2 years ago

mars188 commented 2 years ago

Hello,

I am not sure if there is someone to help with Squire but I write my issue anyway.

I have 8 samples (two groups) that I ran Squire on and obtained individual count tables using "Count". Later, I performed differential expression of TEs with "Call". However, when I looked at the "SQuIRE_gene_TE_counttable.txt" file generated during the "Call" step, it shows different number of TE counts than the "*_TEcounts.txt" file generated during the "Count" step.

Can anyone please explain why is it like that? I was expecting that same count values generated at Count step would be transferred over and different expression would be performed with Call? Confusingly, out of 8 samples, 3 show that TE count values match between "*_TEcounts.txt" and "SQuIRE_gene_TE_counttable.txt" files but not for the rest 5 samples.

Please help!

mars188 commented 2 years ago

Solved with starting from scratch with new environment.