Paired-end sequnces of 16S rRNA are not merged.
Hey there, colleague. I am trying to merge paired-end sequences of 16S rRNA by FLASH software. But, I am getting only less than 3% of merged reads. Why I am getting so low a percent of seqs?
• 927 views
•
link
updated
by
colindaven
•
written
by
shabegmatov •
•
written
by
shabegmatov •
1 answer
They are probably not overlapping enough (read ends are often low quality and thus trimmed off).
You could try the nice nf-core ampliseq pipeline. I had a similar experience with poorly overlapping data and could only use single ended 16S in one project once.
• 0 views
•
link
written
by
colindaven
Log in to answer this question.
More posts like this
-
Need help in using cutadapt to trim paired end fastq reads
written by George •
-
Dada2 in Qiime2: losing reads during merging
written by kamanovae •
-
Merge paired end files for sortmeRNA -- end-goal transcriptome assembly
written by landas •
-
How to process Illumina MiSeq paired-end reads for analysis
written by snow_seq •
-
Merge paired end reads without overlap
written by ahramkim1128 •
-
Low coverage for bases near the end of target reference sequence
written by kspata
-
Paired end reads merged to single end for mapping - should i allow multi-overlap similar to paired …
written by devikaparvathy •
-
IDBA issue 'std::logic_error' SequenceWriter::SequenceWriter() ostream is invalid
written by timothy.ghaly •
-
Chimeric reads identification and removal
written by lakhujanivijay
-
Extracting an information about conservation of 16S rRNA genes of bacteria from multiple sequence a…
written by Peter Leontev
