Hello,
I am wondering why cufflinks is creating transcript model extensions based on low depth of coverage (see the red highlighted box in the attached image). So the reference annotation is in orange and the cufflinks transcript model is in blue.
As you can clearly tell, there is good coverage up to a certain point and suddenly the coverage drops down to 4 reads and cufflinks continues to extend its model to include those 4 reads. Does anyone know how to prevent cufflinks from generating these false extension? And also, if you notice, there is a gap between the area with good coverage and the 4 reads, yet cufflinks thinks this low coverage regions belongs to the previous region with good coverage. Does anyone know why this is occurring and are there parameters that can control for this? Here are the parameters I have used in TopHat and Cufflinks:
Thanks,
I am wondering why cufflinks is creating transcript model extensions based on low depth of coverage (see the red highlighted box in the attached image). So the reference annotation is in orange and the cufflinks transcript model is in blue.
As you can clearly tell, there is good coverage up to a certain point and suddenly the coverage drops down to 4 reads and cufflinks continues to extend its model to include those 4 reads. Does anyone know how to prevent cufflinks from generating these false extension? And also, if you notice, there is a gap between the area with good coverage and the 4 reads, yet cufflinks thinks this low coverage regions belongs to the previous region with good coverage. Does anyone know why this is occurring and are there parameters that can control for this? Here are the parameters I have used in TopHat and Cufflinks:
Code:
#tophat tophat -o tophat_files7 -p 10 --initial-read-mismatches 3 -i 40 -I 50000 -F 0.30 --no-coverage-search -a 10 -g 20 chromosomes_all_4.fastq #cufflinks cufflinks -o cufflinks7 -b CHROMOSOMES_names_ed.fa -I 50000 --min-intron-length 40 --trim-3-avgcov-thresh 3 --trim-3-dropoff-frac 0.4 -p 10 --no-update-check -j 0.05 accepted_hits.bam
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