Hi, all
Recently, I have found that tophat/cufflinks is sensitive to the read name in the alignment.
In a project, I have a sequencing paired-end reads, of which the read names are as follows:
After mapping these reads to the reference by tophat, the read names in the alignment were like:
Obiously, they were different. So when I only used the proper paired reads in the alignment as the input for Cufflinks, I got over 90% genes of 0 FPKM.
After manually changing the name of Read 2 to the same as Read 1, I got a proper result with over 70% genes expressed.
It seems that Tophat/Cufflinks is sensitive to the read name. Dose anyone have experience in this condition?
Recently, I have found that tophat/cufflinks is sensitive to the read name in the alignment.
In a project, I have a sequencing paired-end reads, of which the read names are as follows:
Code:
Read 1: @HWI-ST507:215:C18H0ACXX:2:1101:1831:1943:1:1:0:CGATGT/1 Read 2: @HWI-ST507:215:C18H0ACXX:2:1101:1831:1943:2:1:0:CGATGT/2
Code:
Read 1: @HWI-ST507:215:C18H0ACXX:2:1101:1831:1943:1:1:0:CGATGT Read 2: @HWI-ST507:215:C18H0ACXX:2:1101:1831:1943:2:1:0:CGATGT
After manually changing the name of Read 2 to the same as Read 1, I got a proper result with over 70% genes expressed.
It seems that Tophat/Cufflinks is sensitive to the read name. Dose anyone have experience in this condition?
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