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a problem with RNA-Seq
Hi All.
I have problems with RNA-Seq. We used TruSeq kit to prepare libraries and Tophat to align reads. Take the following two genes as examples to show our problems.
Almost no reads were mapped to exon 1 for Ptf1a.
Many reads were mapped to introns for Rbpjl.
At beginning, we thought it maybe the problem of alignment software. We tried GSNAP. However, the alignements were similar to Tophat.
We suspected there might be some random errors in the experiments. However, when checking our another batch of RNA-Seq data which were done two months ago, we found the alignments were replicable between two batches.
Does anyone have any ideas? Is there anything wrong with our experiments?
Wish your help! Thanks very much! I appreciate it.
I have problems with RNA-Seq. We used TruSeq kit to prepare libraries and Tophat to align reads. Take the following two genes as examples to show our problems.
Almost no reads were mapped to exon 1 for Ptf1a.
Many reads were mapped to introns for Rbpjl.
At beginning, we thought it maybe the problem of alignment software. We tried GSNAP. However, the alignements were similar to Tophat.
We suspected there might be some random errors in the experiments. However, when checking our another batch of RNA-Seq data which were done two months ago, we found the alignments were replicable between two batches.
Does anyone have any ideas? Is there anything wrong with our experiments?
Wish your help! Thanks very much! I appreciate it.
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