Question: Paired-End read merging
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gravatar for genesneuro
2.8 years ago by
genesneuro10
genesneuro10 wrote:

Is it really necessary to do paired-end read merging of forward and reverse reads prior to reference mapping?

sequencing paired end merger • 1.4k views
ADD COMMENTlink modified 2.8 years ago by igor7.4k • written 2.8 years ago by genesneuro10
1
gravatar for igor
2.8 years ago by
igor7.4k
United States
igor7.4k wrote:

No. It is not necessary to merge mate pairs. In fact, it will not always be possible because the read may not overlap. All of the commonly used aligners have an option for processing paired-end data.

Reads may need to be merged for some specialized applications (QIIME, for example), but then that will be explicitly stated.

ADD COMMENTlink written 2.8 years ago by igor7.4k
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gravatar for eldronzhou
2.8 years ago by
eldronzhou350
eldronzhou350 wrote:

If your reads do not overlap (most of cases), there is no need to merge them as most sequence aligners have the option for mapping pair-end reads. Otherwise you may wish to perform read merging (occasionally if you perform pair end small RNA seq), please refer to this thread for more details.

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by eldronzhou350
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