How to remove reads contaminants?

[Guigra]

I'm working with a genome of plant origin. By aligning with the genome sequences of chloroplast and mitochondrial realized that there are contaminants in sequencing.
How to remove them?

[jimmybee]

What are you trying to do? Do you just want the cp and mtDNA?

Why do you say you have contaminants?

[hanshart]

... realized that there are contaminants in sequencing. How to remove them?

Hi Guigra,
without deeply understanding of your problem: If you know the type of contaminant you can always build an index of its corresponding genome/identifier sequences and map all reads to this index at first. The unmapped reads can than be used for the mapping against the genome. But I'm not sure if this is the answer you were looking for.

[Guigra]

Hi hanshart,

Is exactly what I want. How do I do that?

[GenoMax]

Making an index of the contaminats should be straightforward. Once you have the BAM files from those alignments you can recover the unmapped reads following the suggestions in these threads: http://seqanswers.com/forums/showthread.php?t=12283 and http://seqanswers.com/forums/showthread.php?t=30528

[hanshart]

An example for Bowtie:

1. Determine the sequences of your contaminants and write them to a FASTA file like

>seq1
ACGT...
>seq2
GCAG...

(or directly use an available FASTA describing your contaminants)

2. Build a bowtie-index of this FASTA file in a folder called IDX or so:

bowtie-build FASTA IDX/contaminants_idx

3. Map your reads (READFILE) against this contaminants reference and extract unmapped reads (=non-contaminants) to a fastq file (NO_CONTAMINANTS.fastq) directly with the --un flag:

bowtie --un NO_CONTAMINANTS.fastq IDX/contaminants_idx READFILE OUTPUTFILE

The reads in NO_CONTAMINANTS.fastq can finally be mapped against the reference of interest

A non-Bowtie way would be the same: 1. build index for contaminants, 2. map against this index, 3. extract unmapped reads from alignment file to a new fastq file and 4. use only those reads in the new file for the mapping against your reference.

[westerman]

As hanshart says, using bowtie (I actually use bowtie2) is a good -- and easy -- method.

[Guigra]

Thank you all. Were of great help!