Question: Analysis of paired end illumina sequence.
0
gravatar for Surajit
4.3 years ago by
Surajit0
India
Surajit0 wrote:

Hi everyone,

I am  new in NGS.  I would like to filter and identify V4 region from raw paired end Illumina data ( FASTQ format). Please send me suggestion .

Thanks

galaxy • 1.8k views
ADD COMMENTlink modified 4.3 years ago by Bjoern Gruening5.1k • written 4.3 years ago by Surajit0
0
gravatar for Bjoern Gruening
4.3 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi,

this is a very general question. You need to start with the basic NGS analysis, like Quality control (FASTQC), optional trimming and mapping (bowite2, bwa). If you have mapped reads you can convert your BAM file (the mapped reads) to BED file (region) file. This file can be intersected with know regions etc.

I know this answer is also very general but it's quite easy if you search for the keywords mentioned in this text.

Happy research,

Bjoern

ADD COMMENTlink written 4.3 years ago by Bjoern Gruening5.1k
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