% matching problem- RNA_Seq

[sanush]

Hi
I am a new SOLiD user, and completed our first RNA-Seq experiment. I have a question regd the secondary analysis report. For the secondary analysis we uploaded whole human genome as reference and the % matched summary report for our 2 samples were around 25%. But according to ABI the run is considered successful only if the % match is above 30%. Can anyone comment on what the problem might be of low % match.

Thanks

[lmf_bill]

Originally Posted by sanush

Hi
I am a new SOLiD user, and completed our first RNA-Seq experiment. I have a question regd the secondary analysis report. For the secondary analysis we uploaded whole human genome as reference and the % matched summary report for our 2 samples were around 25%. But according to ABI the run is considered successful only if the % match is above 30%. Can anyone comment on what the problem might be of low % match.

Thanks

The mapping percentage is correlated with the mismatches setting, the sequence length and the mapping procedure. You can allow more mismatches and mapping full-length and 1/3 trim-length. maybe, you can got higher percentage. you know, SOLiD generally has more mismatches than Solexa.