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FPKM_tracking File Format

FPKM_tracking files are output by the Cufflinks modules, and contain RNA-seq estimated expression values in Fragments Per Kilobase of transcript per Million mapped reads (FPKM).  For more information on FPKM, see the Cufflinks FAQ.

FPKM tracking files use a generic format to output estimated expression values. Each FPKM tracking file has the following format:

Column number Column name Example Description
1 tracking_id TCONS_00000001 A unique identifier describing the object (gene, transcript, CDS, primary transcript)
2 class_code = The class_code attribute for the object, or "-" if not a transcript, or if class_code isn't present
3 nearest_ref_id NM_008866.1 The reference transcript to which the class code refers, if any
4 gene_id NM_008866 The gene_id(s) associated with the object
5 gene_short_name Lypla1 The gene_short_name(s) associated with the object
6 tss_id TSS1 The tss_id associated with the object, or "-" if not a transcript/primary transcript, or if tss_id isn't present
7 locus chr1:4797771-4835363 Genomic coordinates for easy browsing to the object
8 length 2447 The number of base pairs in the transcript, or '-' if not a transcript/primary transcript
9 coverage 43.4279 Estimate for the absolute depth of read coverage across the object
10 q0_FPKM 8.01089 FPKM of the object in sample 0
11 q0_FPKM_lo 7.03583 the lower bound of the 95% confidence interval on the FPKM of the object in sample 0
12 q0_FPKM_hi 8.98595 the upper bound of the 95% confidence interval on the FPKM of the object in sample 0
13 q0_status OK Quantification status for the object in sample 0. Can be one of OK (deconvolution successful), LOWDATA (too complex or shallowly sequenced), HIDATA (too many fragments in locus), or FAIL, when an ill-conditioned covariance matrix or other numerical exception prevents deconvolution.
14 q1_FPKM 8.55155 FPKM of the object in sample 1
15 q1_FPKM_lo 7.77692 the lower bound of the 95% confidence interval on the FPKM of the object in sample 0
16 q1_FPKM_hi 9.32617 the upper bound of the 95% confidence interval on the FPKM of the object in sample 1
17 q1_status 9.32617 the upper bound of the 95% confidence interval on the FPKM of the object in sample 1. Can be one of OK (deconvolution successful), LOWDATA (too complex or shallowly sequenced), HIDATA (too many fragments in locus), or FAIL, when an ill-conditioned covariance matrix or other numerical exception prevents deconvolution.
3N + 12 qN_FPKM 7.34115 FPKM of the object in sample N
3N + 13 qN_FPKM_lo 6.33394 the lower bound of the 95% confidence interval on the FPKM of the object in sample N
3N + 14 qN_FPKM_hi 8.34836 the upper bound of the 95% confidence interval on the FPKM of the object in sample N
3N + 15 qN_status OK Quantification status for the object in sample N. Can be one of OK (deconvolution successful), LOWDATA (too complex or shallowly sequenced), HIDATA (too many fragments in locus), or FAIL, when an ill-conditioned covariance matrix or other numerical exception prevents deconvolution.

 

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Updated on May 02, 2013 14:44