I am working with a transcriptome of Drosophila melanogaster.
I am using the Hisat2_cufflinks_cuffmerge_cuffdiff methodology however I am having a lot of problems in each issue.
Right now I am confused about remove one replicate of four becouse it seem to be a outlier acording to the genes.read_group_tracking outfile.
If i remove this my results changue and now I have another outlier replicate.
I can understand this and others issues of cufflinks.
Is there someone doing this type of analisis ?
I do that and I got this image, dendogram, https://s18.postimg.org/5xn2g3lh5/file_page1.jpg
The labels " con_spiro " and " sin_spiro " are my treatments , but they are are not grouping in the same "clade
Two of your samples do look like outliers. You can omit them but if you can find out what happened, it will be great.