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Filtering mitochondrion reads from FastQ files

I have fastq files which contains mitochondrion reads. I want to filter out the mitochondrion reads then do the assembly on the resultant reads. Is there a way this can be achieved? Any pointer will be appreciated.

fastq mitochondrion
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updated by Ram Ram • written by javanokendo • javanokendo

Is there a particular reason you need to remove them prior to assembly? Will they cause an issue during assembly?

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written by samuel.a.odonnell samuel.a.odonnell

1 answer

You could simply align your data (use any aligner you like) to the mitochondrial genome and collect reads that do not map. Some aligners can directly separate them for others you may need to filter them out of the resulting BAM alignment file.

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written by GenoMax GenoMax

The following line of code enabled me to filter out mitochondrion reads and I got what I was expecting. I am living it hare because it will help someone.

bbsplit.sh in=HGLGLDSX3_19242446_S3_L001_R1_001.fastq.gz in2=HGLGLDSX3_19242446_S3_L001_R2_001.fastq.gz ref=paradisefishMtsequence.fasta basename=out_%.fastq.gz outu1=mat1.fastq.gz outu2=mat2.fastq.gz
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updated by GenoMax GenoMax • written by javanokendo • javanokendo

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