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Old 05-17-2016, 05:11 PM   #1
Location: India

Join Date: Aug 2015
Posts: 11
Default Bowtie2 reference help

Hi there I am working on paired-end Illumina 2500 data and I wish to check for chloroplast and mitochondrial DNA contamination in it.

My Illumina data is around 1 Gigabases and I have the whole chloroplast genome and also mitochondrial DNA contigs.

My question is -

Will my reference here for bowtie2 for which I have to make the Index be the chloroplast or mitochondrial DNA OR will it be the paired end Illumina data? I am talking about the -x command in bowtie2

I want to compare them so I can remove contaminant chloroplast/mitochondrial DNA.

I was thinking about making the paired end Illumina data as my reference index and then align the relatively shorter chloroplast DNA/ mitochondrial DNA contigs to it. However I have no idea how to make a reference of paired end data even after reading the manual.

Please advise.
Thank you.
Niranjanks is offline   Reply With Quote
Old 05-17-2016, 05:47 PM   #2
Location: India

Join Date: Aug 2015
Posts: 11

Found the answer.

Make a multi fasta file combining the choloroplast and mitochondrial DNA and use it as an index.

Alternatively can just keep the unmapped reads to filter out the contamination.
Niranjanks is offline   Reply With Quote

bowtie2, bowtie2 index

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