Thread: DESeq problems
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Old 08-05-2013, 05:05 AM   #15
vd4mindia
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Location: Milan

Join Date: May 2013
Posts: 40
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I am using the genes.readgrouptracking outpule file of cuffdiff which you can use to create a matrix of the raw fragment counts. I create the matrix from this tracking file output of cuffdiff. Here is a snipplet of it

tracking_id condition replicate raw_frags internal_scaled_frags external_scaled_frags FPKM effective_length status
XLOC_000001 PGT 1 2603 1669.52 1669.52 71.2509 - OK
XLOC_000001 PGT 0 1534 1601.85 1601.85 68.3629 - OK
XLOC_000001 PGT 2 1764 2534.53 2534.53 108.168 - OK
XLOC_000001 PDGT 0 9030 9030 9030 195.012 - OK
XLOC_000001 PDGT 1 4309 4309 4309 93.0574 - OK
XLOC_000002 PGT 1 304 194.98 194.98 8.71171 - OK
XLOC_000002 PGT 0 175 182.74 182.74 8.16483 - OK
XLOC_000002 PGT 2 208 298.856 298.856 13.3529 - OK
XLOC_000002 PDGT 0 1095 1095 1095 24.7572 - OK
XLOC_000002 PDGT 1 835 835 835 18.8788 - OK
XLOC_000003 PGT 1 195 125.07 125.07 14.6047 - OK
XLOC_000003 PGT 0 80 83.5384 83.5384 9.75499 - OK
XLOC_000003 PGT 2 109 156.612 156.612 18.288 - OK
XLOC_000003 PDGT 0 687 687 687 40.595 - OK
XLOC_000003 PDGT 1 454 454 454 26.827 - OK
XLOC_000092 PDGT 1 624 624 624 39.1462 - OK
XLOC_000093 PGT 1 0.666667 0.427588 0.427588 0.0107606 - OK
XLOC_000093 PGT 0 0.5 0.522115 0.522115 0.0131394 - OK
XLOC_000093 PGT 2 1 1.43681 1.43681 0.0361585 - OK
XLOC_000093 PDGT 0 1.66667 1.66667 1.66667 0.0212244 - OK
XLOC_000093 PDGT 1 3.33333 3.33333 3.33333 0.0424487 - OK
XLOC_000094 PGT 1 0 0 0 0 - OK
XLOC_000094 PGT 0 0 0 0 0 - OK
XLOC_000094 PGT 2 0 0 0 0 - OK
XLOC_000094 PDGT 0 0 0 0 0 - OK
XLOC_000094 PDGT 1 0 0 0 0 - OK
XLOC_000095 PGT 1 6 3.84829 3.84829 0.0342992 - OK
XLOC_000095 PGT 0 11.4802 11.9879 11.9879 0.106847 - OK
XLOC_000095 PGT 2 4.56786 6.56314 6.56314 0.0584964 - OK
XLOC_000095 PDGT 0 8.49762 8.49762 8.49762 0.0383257 - OK
XLOC_000095 PDGT 1 7.22143 7.22143 7.22143 0.0325698 - OK


the 4th coulmn is the raw fragment count and as you can see some of the values are having decimal values.
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