User: WZOUXM

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WZOUXM10
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Posts by WZOUXM

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Comment: C: Tophat problem - R1 and R2 reads mapped to different strandeds of viral genome
... Actually, if I only analyze single-end reads (either R1 or R2), then I did not see the problem. And I get reads for both positive and negative strands. ...
written 7 days ago by WZOUXM10
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Comment: C: Tophat problem - R1 and R2 reads mapped to different strandeds of viral genome
... Hi Charles, Thank you for your reply. The libraries were prepared with a TruSeq stranded total RNA sample with a Ribo‐Zero prep kit. I understand the R1 and R2 should show a separate trend. But for my project, both strands of the double stranded virus genome transcript viral genes. So there are mRN ...
written 7 days ago by WZOUXM10
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Comment: C: Tophat problem - R1 and R2 reads mapped to different strandeds of viral genome
... Hi, thank you all for response. Actually I agree with you. I tried Hisat using the following command to analyze my data and give me the same results as Tophat. And I still can not find the reason. hisat2 -p 7 -S 1.sam -x ref.fa -1 R1.fq.gz -2 R2.fq.gz ...
written 7 days ago by WZOUXM10
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Tophat problem - R1 and R2 reads mapped to different strandeds of viral genome
... We recently analyze a set of RNA-seq data with Tophat and met some questions about the alignment. We infected cells with virus and extracted total RNA samples for RNA-seq at different time points. Libraries were prepared with a TruSeq stranded total RNA sample with a Ribo‐Zero prep kit, and the RN ...
software error alignment rna-seq written 11 days ago by WZOUXM10 • updated 7 days ago by Charles Warden5.8k

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