Problems with call output

wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression

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Problems with call output #58

Closed fernandogs97 closed 3 years ago

fernandogs97 commented 3 years ago

Hello, after performing some TE analysis in the mouse (analyzed against the mm39 version) I have obtained an erroneous call output in which several headers are missing, preventing the correct recognition of the data. Anyone else has happened? imagen

mars188 commented 3 years ago

Hi,

Were you able to find an explanation for such an output? I obtained the similar output and not sure how to recognize the TE in this.

Please let me know. Many thanks!

fernandogs97 commented 3 years ago

Hello mars188, finally I noticed that the only think that you need to do is to move the headers 2 columns right for having the correct information, it is not a problem of squire, it also happen with deseq2 when you perform the differential expression analysis of genes. PD: The second column indicate the strand information if the data is stranded, as I perfomed the analysis with unstranded date its "." as it doesn't report that information.