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.
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!