More guidelines for pre-processing step please

[mabelwong]

According to the paper, 'As a pre-requisite for binning, the user must create BAM files by aligning the reads of each sample separately to the assembled metagenome'

As a non bioinformatician who is trying to work through some metagenomics data, I am confused... May I ask:

• Can I use this software for my data please? I have 6 different samples in total, and 1 illumina PE run per sample. I would like to perform genome binning per sample.

• How to create BAM files please? I have the raw Illumina reads, and assembled reads generated by Abyss.

I am not sure whether this is the place for asking questions, but this is the closest thing to a Q&A forum I find here. Sorry in advance if the message shouldn't be posted here. Your answer will be greatly appreciated.

Thank you very much, Mabel

[Rob Egan]

Yes you absolutely can use metabat on your data. I recommend generating 6 separate bams, one for each sample/Illumina run. Generating BAMs is outside the scope of Metabat, but I it is easy to do, and there are many ways to do it if you search google and the seqansers forums: http://seqanswers.com.

I recommend downloading and installing bwa and samtools. You can use bwa to align your reads (recommend the mem module) into a SAM file, and then use samtools to convert the SAM into a sorted BAM file.

bwa index reference.fasta bwa mem [options] reference.fasta <in1.fq> [in2.fq] > in.fq.sam samtools view -Sbu in.fq.sam | samtools sort - in.fq.sam

Repeat for each sample, then you can use the reference.fasta and the resulting 6 different *.fq.sam.bam files and the as input into runMetabat.sh