Cuffdiff output file

[songyj]

hi,

When I using Cufflinks-Cuffcompare-Cuffdiff to analysis my RNA-seq data, I found a question.

In cuffdiff output file, gene_exp.diff, usually "A gene name" have more than one different locus even in different chr.

It make me confused, it isn't a gene have a record in gene_exp.diff ?

like gene U6, in gene_exp.diff, they have

XLOC_000130     XLOC_000130     U6      chr1:23488591-23489575  q1      q2      NOTEST  1.17921 0.489751        -1.2677 1.41199 0.157954        1       no
XLOC_007133     XLOC_007133     U6      chr10:29046365-29050865 q1      q2      NOTEST  0.715357        0.493826        -0.534662       0.598727        0.549355     1       no
XLOC_011686     XLOC_011686     U6      chr12:51556268-51557200 q1      q2      NOTEST  1.89382 0.749147        -1.33798        1.87499 0.0607936       1   no
XLOC_014629     XLOC_014629     U6      chr13:73454957-73456810 q1      q2      NOTEST  0.946175        0.166244        -2.50881        2.26666 0.0234107   no
XLOC_057577     XLOC_057577     U6      chr9:556306-562036      q1      q2      NOTEST  2.21376 1.26377 -0.808767       1.98748 0.0468697       1       no
XLOC_057725     XLOC_057725     U6      chr9:97269425-97271417  q1      q2      NOTEST  1.39023 0.61348 -1.18024        2.1936  0.0282639       1       no
XLOC_060262     XLOC_060262     U6      chrX:123007615-123008869        q1      q2      NOTEST  1.20754 0.364642        -1.72752        1.98409 0.0472457   no

thanks,
song

[dpryan]

You'll find there are many copies of a lot of the snRNAs (and tRNAs and others) throughout the genome.

[songyj]

thanks

You'll find there are many copies of a lot of the snRNAs (and tRNAs and others) throughout the genome.

I try to used "Test status" to filter data, only choose "test status" as "OK"

Thanks again!