Dear All,
I'm just got my RNA-seq result back but I'm new to analysis. I decided to try it out following the tuxedo protocol. After alignment with Tophat2 following quality trimming, I got relatively low mapping rate (~50%-60% ). I'm not sure what's the cause. I'm thinking about cleaning the data such as trimming the adapter before doing the alignment. I can tell the fastQC report doesn't looks so good but have no idea where to start. Can anyone have a look at the report and give me some suggestions? The libraries are prepared using integenX kit after rRNA depletion and we sequenced them by PE100. Thanks.
Jason
I'm just got my RNA-seq result back but I'm new to analysis. I decided to try it out following the tuxedo protocol. After alignment with Tophat2 following quality trimming, I got relatively low mapping rate (~50%-60% ). I'm not sure what's the cause. I'm thinking about cleaning the data such as trimming the adapter before doing the alignment. I can tell the fastQC report doesn't looks so good but have no idea where to start. Can anyone have a look at the report and give me some suggestions? The libraries are prepared using integenX kit after rRNA depletion and we sequenced them by PE100. Thanks.
Jason
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