Question: MinION: To remove reads that mapped towards a custom database
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gravatar for fang-shiang.lim
6 weeks ago by
fang-shiang.lim10 wrote:

Hi all,

I am very new on bioinformatics. I will be running MinION in the near future and I have a question which I still couldn't figure out the solution. As part of the post sequencing analysis of the MinION data, I wish to remove parts of the reads that have been mapped/assigned to a custom database (in this case will be the host genome data) so that I am left with the non-host reads for further analysis. Any idea which software can do so?

Thank you very much in advance!

Lim

next-gen • 132 views
ADD COMMENTlink modified 6 weeks ago by genomax89k • written 6 weeks ago by fang-shiang.lim10
0
gravatar for genomax
6 weeks ago by
genomax89k
United States
genomax89k wrote:

You will need at least two package. An aligner (minimap2) to align the data initially. Then samtools to retrieve reads that do not map to your custom database. In first two commands 4 threads are being used (-t and -@).

$ minimap2 -x map-ont -t 4 -a -o data_out.sam your_ref.fasta data_input.fastq
$ samtools sort -@ 4 -o data_out_sorted.bam data_out.sam
$ samtools view -f 4 G_data_out_sorted.bam | samtools bam2fq - > unmapped.fastq
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by genomax89k

Thank you very much. Will give it a try!

ADD REPLYlink written 6 weeks ago by fang-shiang.lim10
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