joining paired end illumina data for metagenomic analysis
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
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
STACKS pipeline. Confused about paired-end with "ustacks".
written by Roland •
-
Combining unpaired and paired-end reads in spades assembly
written by rescueson •
-
Use pre-assembled paired-end reads as single-end for metagenome assembly with metaSPAdes
written by somnja •
-
Reference OTU-picking using pair-end reads without merging
written by Eli Korvigo
-
Which file can be upload in MG-RAST
written by hafroz01 •
-
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
written by dllopezr •
-
Forward and Reverse Reads Out of Order
written by dw845316 •
-
When paired end reads doesn't join, can i consider them single-end in metagenomic analysis?
written by fernandalpcosta •
-
QIIME - Illumina MiSeq, Paired-end Data - Mapping file and Data Preprocessing Questions
written by sarajeanne08 •
-
How to deal with demultiplexed Miseq pair-end (2*250bp) 16S data using QIIME?
written by nkuyfq
Give
bbmerge.shfrom 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.thanks a lot genomax. I tried
bbmerge.shbut got same result.can I put Ns between two reads to link them? it is 2x250 reads, and insert length is approximately 420.