Cuffdiff Output file question

Question

[sumitra.20]

Hi,

I followed through the tophat-cufflink pipeline for my test data (3 samples). I merged all my samples with cuffmerge and ran cuffdiff as below:

cuffdiff -o ./cuffdiff_output_testdata -L hyp,lyp -p 8 -b Oryza_indica.ASM465v1.dna_sm.toplevel.fa ./cuffmerge_output/merged.gtf /R32P1_R4_ensembl_GTF_tophat_out/accepted_hits.bam,/R32P3_R4_ensembl_GTF_tophat_out/accepted_hits.bam /R34P4_R_ensembl_GTF_tophat_out/accepted_hits.bam

I gt several output files, but im confused with the replicate 'genes.read_group_tracking' file (as shown in the image attached). I have 3 samples belonging to 2 groups hyp and lyp, where hyp has 2 replicates and lyp only has 1 sample. But why does the column replicate has 3 rows for each tracking_id indicating the replicate is 0,1,0? Just worried if the command i ran for cuffdiff is wrong

[dsull]

no one uses tophat-cuffdiff nowadays and it's no longer being maintained/supported.

How about upgrading your pipeline to something more recent?

[sumitra.20]

hey, i changed to a different pipeline using hisat2-stringtie. Thank you