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Hi,all:
I am using tophat and cufflinks to analysis my RNA-seq datas recently, but I encountered some problems,so I need your helps.The problems are as below：
1, My RNA-seq datas are pair-ends reads, but mate 2 have 9 linker bases in the head, so I trimed the 9 bases, and now mate 1 is 51bp and mate 2 is 42bp, so my question is that can tophat run these datas correctly. Can tophat be used to deal with the situation of two mates having different reads length?
2 , Since my reads length is 42 bp, what number can be set to the parameter "--segment-length" ? And what about the parameter "--min-anchor".
I am using tophat and cufflinks to analysis my RNA-seq datas recently, but I encountered some problems,so I need your helps.The problems are as below：
1, My RNA-seq datas are pair-ends reads, but mate 2 have 9 linker bases in the head, so I trimed the 9 bases, and now mate 1 is 51bp and mate 2 is 42bp, so my question is that can tophat run these datas correctly. Can tophat be used to deal with the situation of two mates having different reads length?
2 , Since my reads length is 42 bp, what number can be set to the parameter "--segment-length" ? And what about the parameter "--min-anchor".