Hello,
I was trying to compare RNA-seq samples run on the solid platform and the GA platform.
I aligned my GA data on using Tophat.
My Solid data was aligned using bioscope.
Then both samples were analyzed using Cufflinks and Cuffcompare.
My question is, on my .loci file, i have strandness information about my GA read that align to non-annotated areas. This should not be possible because my GA library was paired-end, hence no directionality.
My Solid data on the other hand seems to be lacking a lot of strandness information. Edit: my Solid reads were adapted specifically to have directionality.
Can anyone tell me what is going on? Thanks in advance.
I was trying to compare RNA-seq samples run on the solid platform and the GA platform.
I aligned my GA data on using Tophat.
My Solid data was aligned using bioscope.
Then both samples were analyzed using Cufflinks and Cuffcompare.
My question is, on my .loci file, i have strandness information about my GA read that align to non-annotated areas. This should not be possible because my GA library was paired-end, hence no directionality.
My Solid data on the other hand seems to be lacking a lot of strandness information. Edit: my Solid reads were adapted specifically to have directionality.
Can anyone tell me what is going on? Thanks in advance.
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