Cuffdiff: How to see the FPKM of each gene in each one of the samples in the groups?

Question

[juafonso_bio]

In the Cuffdiff outputs I can see the FPKM of each gene in the groups, but how can I get the FPKM of each gene in each one of the samples in the groups???

[Istvan Albert]

As far as I know that information is not available. Very annoying.

Edit: apparently that information is available though well hidden from view! Will the wonders every cease!

Answer 1

[ablanchetcohen]

As juafonso_bio has already found out, the FPKM values in the output of Cuffdiff can be found in the file genes.read_group_tracking. The replicates are identified by numbers, starting at 0. The correspondance between the replicate number and the sample name can be found in the file read_groups.info.

Here is an example.

-bash-4.1$ more genes.read_group_tracking 
tracking_id condition   replicate   raw_frags   internal_scaled_frags   external_scaled_frags   FPKM    effective_length    status
ENSMUSG00000000001  shCas1  2   8025    6474.79 6474.79 56.6616 -   OK
ENSMUSG00000000001  shCas1  0   6508    6724.17 6724.17 58.844  -   OK
ENSMUSG00000000001  shCas1  1   4740    5932.42 5932.42 51.9153 -   OK
ENSMUSG00000000001  shRnf2_388  0   7579    7162.23 7162.23 62.6775 -   OK
ENSMUSG00000000001  shRnf2_388  1   6783    7142.23 7142.23 62.5025 -   OK
ENSMUSG00000000001  shRnf2_388  2   7982    6855.53 6855.53 59.9935 -   OK
ENSMUSG00000000001  Casz1v2 0   7719    8440.91 8440.91 73.8673 -   OK
ENSMUSG00000000001  Casz1v2 1   6487    7135.16 7135.16 62.4406 -   OK
ENSMUSG00000000001  Casz1v2 2   7712    7013.6  7013.6  61.3768 -   OK
ENSMUSG00000000001  pSiren  1   6116    6064.53 6064.53 53.0714 -   OK
ENSMUSG00000000001  pSiren  0   7557    6877.29 6877.29 60.1839 -   OK
ENSMUSG00000000001  pSiren  2   6151    6762.49 6762.49 59.1793 -   OK

-bash-4.1$ more read_groups.info 
file    condition   replicate_num   total_mass  norm_mass   internal_scale  external_scale
../../results/tophat/shCas1_1/accepted_hits.bam shCas1  0   3.24875e+07 3.5031e+07  0.967852    1
../../results/tophat/shCas1_2/accepted_hits.bam shCas1  1   2.96395e+07 3.5031e+07  0.798999    1
../../results/tophat/shCas1_3/accepted_hits.bam shCas1  2   4.18947e+07 3.5031e+07  1.23942 1
../../results/tophat/shRnf2_388_1/accepted_hits.bam shRnf2_388  0   3.64417e+07 3.5031e+07  1.05819 1
../../results/tophat/shRnf2_388_2/accepted_hits.bam shRnf2_388  1   3.28269e+07 3.5031e+07  0.949703    1
../../results/tophat/shRnf2_388_3/accepted_hits.bam shRnf2_388  2   4.05007e+07 3.5031e+07  1.16432 1
../../results/tophat/Casz1v2_1/accepted_hits.bam    Casz1v2 0   3.22445e+07 3.5031e+07  0.914475    1
../../results/tophat/Casz1v2_2/accepted_hits.bam    Casz1v2 1   3.26844e+07 3.5031e+07  0.909159    1
../../results/tophat/Casz1v2_3/accepted_hits.bam    Casz1v2 2   3.91855e+07 3.5031e+07  1.09958 1
../../results/tophat/pSiren_1/accepted_hits.bam pSiren  0   3.79887e+07 3.5031e+07  1.09883 1
../../results/tophat/pSiren_2/accepted_hits.bam pSiren  1   3.63825e+07 3.5031e+07  1.00849 1
../../results/tophat/pSiren_3/accepted_hits.bam pSiren  2   3.15436e+07 3.5031e+07  0.909576    1

Answer 2

[juafonso_bio]

Found it. The FPKM of each gene in each one of the samples in the group (replicates) is at the genes.read_group_tracking, an output of Cufflinks. This information can also be found in the .estim_out files that are outputs of Stringtie, but them you need to open each file in the analysis of each sample.

[Istvan Albert]

thanks for following up!