Question: joining paired end illumina data for metagenomic analysis
0
gravatar for cvu
2.7 years ago by
cvu150
India
cvu150 wrote:

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

ADD COMMENTlink written 2.7 years ago by cvu150
2

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 REPLYlink written 2.7 years ago by genomax77k

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

ADD REPLYlink written 2.7 years ago by cvu150

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

ADD REPLYlink written 2.7 years ago by cvu150
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