Hi everyone,
I am working on a species with little genome information available. I had 4 samples of RNA-seq. I would like to know how many genes were differentially expressed among these 4 samples. We used illumina GAII 100bp paired-end sequencing. First, I combined the all sequences to one single file (all left to one single left file and all right to one single right file). Using the combined sequences to do denovo assembly by trinity. Then, I mapped the sample sequences to the assembled sequences. However, I got very low map rate (about 2%) using paired-end sequences. If I used single-end sequence to map, I got about 40% mapping rate. What's the possible problem? It bothered me a whole week now. Thank you in advance for your help!
Yan
I am working on a species with little genome information available. I had 4 samples of RNA-seq. I would like to know how many genes were differentially expressed among these 4 samples. We used illumina GAII 100bp paired-end sequencing. First, I combined the all sequences to one single file (all left to one single left file and all right to one single right file). Using the combined sequences to do denovo assembly by trinity. Then, I mapped the sample sequences to the assembled sequences. However, I got very low map rate (about 2%) using paired-end sequences. If I used single-end sequence to map, I got about 40% mapping rate. What's the possible problem? It bothered me a whole week now. Thank you in advance for your help!
Yan
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