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I tried the option to emit count tables in cuffdiff. I expected the counts to be integers, but I get fractions. Are these normalized counts?
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Yes, these are the result of "common scale transformation" of counts. See the DESeq paper for how these are computed - we do the same thing to transform all counts across the replicates for a condition to a common scale for that replicate before fitting the dispersion model. -
about --emit-count-tables
Hi Cole and PFS,
I have some questions about --emit-count-tables option, which is said that
"Cuffdiff will output a file for each condition (called <sample>_counts.txt)".
I run Cuffdiff with 4 samples' bam file together, but I got only locus_var.txt and pooled_counts.txt.
Q1, what does pooled_counts.txt indicate?
Q2, in locus_var.txt, the number of condition column indicates each samples in the same order as those in cuffdiff command line?
*Here is my command,
cuffdiff -p 2 -u --emit-count-tables ./../compare/cuffcmp.combined.gtf ./../Nipponbare/tophat_out/accepted_hits.bam ./../Kasalath/tophat_out/accepted_hits.bam ./../Nip_Kas/tophat_out/accepted_hits.bam ./../Kas_Nip/tophat_out/accepted_hits.bam
*the content of locus_var.txt
0 TCONS_00005163 1348.57 15275.1 132648 50019.6 30 3 0 0 0.219325 0 0 0 0 -1.0565
0 TCONS_00005164 1348.57 15275.1 132648 50019.6 30 3 0 0 0.0778509 0 0 0 0 0.0389116
1 TCONS_00000001 1348.57 15275.1 132648 96366.6 30 3 0 0 0.751663 0 0 0 0 0.676941
1 TCONS_00005163 1348.57 15275.1 132648 96366.6 30 3 0 0 0.00888725 0 0 0 0 -5.68775
1 TCONS_00005164 1348.57 15275.1 132648 96366.6 30 3 0 0 0.240978 0 0 0 0 1.74781
2 TCONS_00000001 1348.57 15275.1 132648 94122.3 30 3 0 0 0.699411 0 0 0 0 0.572296
2 TCONS_00005163 1348.57 15275.1 132648 94122.3 30 3 0 0 0.223565 0 0 0 0 -1.03559
2 TCONS_00005164 1348.57 15275.1 132648 94122.3 30 3 0 0 0.0784949 0 0 0 0 0.138381
0 TCONS_00005166 55.532 1915.14 986.219 19.6345 30 4 0 0 0 0 0 0 0 -inf
0 TCONS_00006797 55.532 1915.14 986.219 19.6345 30 4 0 0 0.996369 0 0 0 0 2.04356
0 TCONS_00006796 55.532 1915.14 986.219 19.6345 30 4 0 0 0.503341 0 0 0 0 1.0567
0 TCONS_00005165 55.532 1915.14 986.219 19.6345 30 4 0 0 0.00028983 0 0 0 0 -9.7241
3 TCONS_00000001 1348.57 15275.1 132648 158408 30 3 0 0 0.676484 0 0 0 0 0.521408
The each numbers of condition column are corresponding to...
0 -> Nipponbare
1 -> Kasalath
2 -> Nip_Kas
3 -> Kas_Nip
correct?
And one more question, after grouping this file into each sample_txt by condition number and sorting by description, I got 2 same records like this..
0 TCONS_00000001 1348.57 15275.1 132648 50019.6 30 3 0 0 0.703948 0 0 0 0 0.588801
0 TCONS_00000001 1348.57 15275.1 132648 50019.6 30 3 0 0 0.703948 0 0 0 0 0.588801
0 TCONS_00000002 3202.34 180770 597601 89875.9 30 8 0 0 0.00282914 0 0 0 0 -4.4797
0 TCONS_00000002 3202.34 180770 597601 89875.9 30 8 0 0 0.00282914 0 0 0 0 -4.4797
0 TCONS_00000005 885.268 8618.77 68982.9 14506.8 30 3 0 0 0.440866 0 0 0 0 0.181828
0 TCONS_00000005 885.268 8618.77 68982.9 14506.8 30 3 0 0 0.440866 0 0 0 0 0.181828
Why are there same records??
If possible, please describe the details about each columns of locus_var.txt?
I really appreciate any your helps,
zunComment
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Cole, Thanks for the clarification. By any chance, are the raw counts available in the intermediate temp files generated by cuffdiff ? Thanks.Originally posted by Cole Trapnell View PostComment
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