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???
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???
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
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.
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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!