I'm running Cufflinks (2.2.1) on a set of RNA-seq alignments that I did with STAR. I'm using these options:
In every instance I get the message: "WARNING: Multi-Hit not found". I pasted the beggining of the output of a run I did.
In this particular library, I got the warning 1997 times.
What is happening? Should I add a option to Cufflinks?
Code:
/home/user1/Data/Softwares/cufflinks-2.2.1/cufflinks -p 6 -u -o ./Cufflinks/ERR036348_pass-2 ./Alignments/ERR036348_pass-2/ERR036348_pass-2_Aligned.sortedByCoord.out.bam
Code:
[00:12:17] Inspecting reads and determining fragment length distribution. > Processed 51509 loci. [*************************] 100% > Map Properties: > Normalized Map Mass: 28150478.05 > Raw Map Mass: 28150478.05 > Number of Multi-Reads: 2479202 (with 6180369 total hits) > Fragment Length Distribution: Empirical (learned) > Estimated Mean: 353.78 > Estimated Std Dev: 35.57 [01:36:09] Assembling transcripts and initializing abundances for multi-read correction. > Processing Locus 1:86701401-87057627 [ ] 2% WARNING: Multi-Hit not found (86357258,86357334). WARNING: Multi-Hit not found (86357265,86357341). WARNING: Multi-Hit not found (86357276,86357352).
What is happening? Should I add a option to Cufflinks?