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Dear Community,
I recently had sequencing data from stranded library (second strand). The count output from STAR indicated that most of the reads mapped to the second strand. I then ran cuffdiff using the bam files from STAR with -library-type parameter specified.
I happened to find that the either -library-type fr-firststrand or -library-type fr-secondstrand give the fpkms. How should I explain this?
For example:
0610009B22Rik, has 131 reads mapped to the second strand, and only 1 read mapped to the first strand (from STAR count file)
however, it has fpkm of 10.05 when I used "-library-type fr-firststrand", but fpkm of 2.32 when I used "-library-type fr-secondstrand". My expectation was that the latter should be much higher than the former...
Could anyone provide some inputs?
Thanks a lot!
C.
I recently had sequencing data from stranded library (second strand). The count output from STAR indicated that most of the reads mapped to the second strand. I then ran cuffdiff using the bam files from STAR with -library-type parameter specified.
I happened to find that the either -library-type fr-firststrand or -library-type fr-secondstrand give the fpkms. How should I explain this?
For example:
0610009B22Rik, has 131 reads mapped to the second strand, and only 1 read mapped to the first strand (from STAR count file)
however, it has fpkm of 10.05 when I used "-library-type fr-firststrand", but fpkm of 2.32 when I used "-library-type fr-secondstrand". My expectation was that the latter should be much higher than the former...
Could anyone provide some inputs?
Thanks a lot!
C.