Hi
I am analysing RNA-Seq data using the Tophat2/Cufflinks2(Cuffdiff2) pipeline. This has worked well for several projects, however for this project I am only getting differentially expressed genes output if I omit the fragment length bias correction step.
I have run the Tophat2 output through Cuffdiff v1.3.0 with fragment length bias correction on and the program output significantly expressed genes.
Blow is the command I would like to run
cuffdiff2 -o bombyx_tophat2_cuffdiff2_out -b /data2/genomes/bowtie2_indexes/B_mori/B_mori.fa -p 12 -L anterior,posterior -u /data2/genomes/bowtie2_indexes/B_mori/Annotation/B_mori.gff /data2/graham/julian_dow/bombyx/FC052_s1_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s4_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s5_tophat2_Bm/accepted_hits.bam /data2/graham/julian_dow/bombyx/FC052_s6_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s7_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s8_tophat2_Bm/accepted_hits.bam
But I have to run this command to get any significant genes
cuffdiff2 -o bombyx_tophat2_cuffdiff2_out -p 12 -L anterior,posterior -u /data2/genomes/bowtie2_indexes/B_mori/Annotation/B_mori.gff /data2/graham/julian_dow/bombyx/FC052_s1_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s4_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s5_tophat2_Bm/accepted_hits.bam /data2/graham/julian_dow/bombyx/FC052_s6_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s7_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s8_tophat2_Bm/accepted_hits.bam
Can anyone tell me why this is happening?
Graham
I am analysing RNA-Seq data using the Tophat2/Cufflinks2(Cuffdiff2) pipeline. This has worked well for several projects, however for this project I am only getting differentially expressed genes output if I omit the fragment length bias correction step.
I have run the Tophat2 output through Cuffdiff v1.3.0 with fragment length bias correction on and the program output significantly expressed genes.
Blow is the command I would like to run
cuffdiff2 -o bombyx_tophat2_cuffdiff2_out -b /data2/genomes/bowtie2_indexes/B_mori/B_mori.fa -p 12 -L anterior,posterior -u /data2/genomes/bowtie2_indexes/B_mori/Annotation/B_mori.gff /data2/graham/julian_dow/bombyx/FC052_s1_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s4_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s5_tophat2_Bm/accepted_hits.bam /data2/graham/julian_dow/bombyx/FC052_s6_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s7_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s8_tophat2_Bm/accepted_hits.bam
But I have to run this command to get any significant genes
cuffdiff2 -o bombyx_tophat2_cuffdiff2_out -p 12 -L anterior,posterior -u /data2/genomes/bowtie2_indexes/B_mori/Annotation/B_mori.gff /data2/graham/julian_dow/bombyx/FC052_s1_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s4_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s5_tophat2_Bm/accepted_hits.bam /data2/graham/julian_dow/bombyx/FC052_s6_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s7_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s8_tophat2_Bm/accepted_hits.bam
Can anyone tell me why this is happening?
Graham