Combining paired reads with same coordinates

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6.7 years ago

hmkvsri • 0

Dear All,

Is there a tool which combines the reads with same coordinates from an illumina pair end raw data. I used Pear but it seems to combine sequences which does not have identical coordinates. I also tried fastqCombinePairedEnd.py by Eric Normandeau, but I dint get any output.

Thank you Regards kavya

sequencing Assembly • 1.2k views

ADD COMMENT • link 6.7 years ago by hmkvsri • 0

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Hello,

do you realy want to combine those reads or do you want to remove those duplicates? The last one you can do with picard MarkDuplicates.

fin swimmer

ADD REPLY • link 6.7 years ago by finswimmer 16k

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Hi , The data is a from saturation mutagenesis experiment and not a genomic sequencing data. So there could either be one or two genes with single or double mutants. Some of the papers I have seen people using Pear on the raw data for processing. Does it combine based on coordinates? Regards

ADD REPLY • link 6.7 years ago by hmkvsri • 0

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Does it combine based on coordinates?

If the coordinates that you are referring to are for the individual clusters (sequenced from two ends) then yes. A cluster is formed from a single library fragment. BBMerge from BBMap Suite will do the merging.

For reads to actually merge there has to be an overlap in the middle of the sequenced fragment. If your library insert sizes are longer than sequence length (cycles) then the reads are not going to merge/overlap directly.