Question: Can I Convert Paired-End Datasets Into Single End Ones?
gravatar for Du, Jianguang
6.3 years ago by
Du, Jianguang380
Du, Jianguang380 wrote:
Dear All, I have some paired-end datasets to be analyzed, but I am not sure about their Mean Inner Distance between Mate Pairs. Can I convert these paired-end datasets into single-end ones and use them as single-end dataset as follows? 1) Use the tool "Manipulate FASTQ" to convert the sequence of reverse reads into its reverse-complement counter part, so that all of the reverse reads actually become forward reads. 2) run Tophat on the manipulated datasets as single-end ones. Thanks. Jianguang
rna-seq tophat • 2.2k views
ADD COMMENTlink modified 6.3 years ago by Jennifer Hillman Jackson25k • written 6.3 years ago by Du, Jianguang380
gravatar for Jennifer Hillman Jackson
6.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Jianguang, This is not recommended. The value of the paired relationships would be lost. Using an estimated Mean Inner Distance is a much better solution. This is keeping in mind that testing different values may be necessary to obtain the optimal results for any dataset. Your situation about the reported vs actual sizing is not unique and does not mean that the data is poor (when considered as a single factor). Searching an online NGS website such as about the topic will being up several threads where this is discussed. Should you have outstanding concerns about this particular parameter, please consider contacting the tool authors at for advice. Best, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 6.3 years ago by Jennifer Hillman Jackson25k
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