Question: paired end quality filtering
1
gravatar for sun.nation
3.6 years ago by
sun.nation120
United States
sun.nation120 wrote:

I know it has been asked earlier but not able to find clear solution. I need to filter paired fastq files and align using bowtie2. Is there any tools that I am missing to filter fastq files and keep only paired-end in two different files. And, remaining single reads in another file?

Thanks

SS

filter paired end fastq illumina • 2.9k views
ADD COMMENTlink modified 3.6 years ago by h.mon24k • written 3.6 years ago by sun.nation120

Here is a great solution from Heng Li: A: Combining The Paired Reads From Illumina Run

ADD REPLYlink written 3.6 years ago by Ashutosh Pandey11k
1
gravatar for Dan D
3.6 years ago by
Dan D6.7k
Tennessee
Dan D6.7k wrote:

I recommend sickle.

ADD COMMENTlink written 3.6 years ago by Dan D6.7k
0
gravatar for h.mon
3.6 years ago by
h.mon24k
Brazil
h.mon24k wrote:

What do you mean by "filter"? Quality trimming? Adapter removal? Contaminant filtering? All of them?

BBDuk and SeqyClean will do all, and will keep proper pairs and a file with singles.

ADD COMMENTlink written 3.6 years ago by h.mon24k

yes quality trimming

ADD REPLYlink written 3.6 years ago by sun.nation120
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