Dear Pantelis,

the updated analysis of run44 has
tracks at:
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/PHlab/run44/mm10/www/hub.txt

At
http://genomics-lab.fleming.gr/fleming/PHlab/run44/mm10/www/cuffdiff_villi_vs_crypts2/isoform_exp.diff.xlsx
is the cufflinks/diff analysis for isoforms with biotypes and class_codes, which are defined as follows:

Priority	Code	Description
1	=	Complete match of intron chain
2	c	Contained
3	j	Potentially novel isoform (fragment): at least one splice junction is shared with a reference transcript
4	e	Single exon transfrag overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment.
5	i	A transfrag falling entirely within a reference intron
6	o	Generic exonic overlap with a reference transcript
7	p	Possible polymerase run-on fragment (within 2Kbases of a reference transcript)
8	r	Repeat. Currently determined by looking at the soft-masked reference sequence and applied to transcripts where at least 50% of the bases are lower case
9	u	Unknown, intergenic transcript
10	x	Exonic overlap with reference on the opposite strand
11	s	An intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors)
12	.	(.tracking file only, indicates multiple classifications)


BW,
Martin