This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Combining paired reads with same coordinates

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
• 1,731 views • link
written by hmkvsri • hmkvsri

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

• 0 views • link
written by finswimmer finswimmer

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

• 0 views • link
written by hmkvsri • hmkvsri

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.

• 0 views • link
written by GenoMax GenoMax

Thank you I will try it. Regards

• 0 views • link
written by hmkvsri • hmkvsri

0 answers

No answers yet.

Log in to answer this question.

More posts like this