joining paired end illumina data for metagenomic analysis

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7.5 years ago

cvu ▴ 180

Hello people,

I've paired end 16s metagenomic data. I tried to join forward and reverse reads with join_paired_ends.py but 50% data was assembled and I'm loosing 50% of my data which comes in fastqjoin.un1.fastq and fastqjoin.un2.fastq. I think my reads are not overlapping there must be gap between two reads.

In this case how can I analyse metagenomic 16s data, since most of the metagenomic analysis tools accept single end data (eg. QIIME).

Thanks

metagenome 16s QIIME paired end illumina • 3.0k views

ADD COMMENT • link 7.5 years ago by cvu ▴ 180

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Give bbmerge.sh from BBMap suite a try. If you used an established protocol for this experiment then most of the reads should merge. You can find usage directions in this thread.

ADD REPLY • link 7.5 years ago by GenoMax 147k

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thanks a lot genomax. I tried bbmerge.sh but got same result.

ADD REPLY • link 7.5 years ago by cvu ▴ 180

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can I put Ns between two reads to link them? it is 2x250 reads, and insert length is approximately 420.

ADD REPLY • link 7.5 years ago by cvu ▴ 180

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