Alignment of genomic resequenced data to reference genome
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6.5 years ago
kirannbishwa01 ★ 1.3k

I am working with population specific re-sequenced genome data from A. lyrata. I need to align it to the reference genome which is already available and prepare population specific sequence. I will also do variant calling but for now alignment of fragment to reference genome is what I am interested in.

Could anyone suggest of a pipeline/apps combination that would be helpful for this purpose?

Thanks,

sequencing alignment genome A.lyrata Assembly • 1.5k views
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Did you look at (read Google) the tools available for short read alignment?

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6.5 years ago
TriS ★ 4.4k

I like bowtie2, you can find the manual here. from the results files you can then use SAMTools BCFtools to find variants.

as a VERY general guide your steps should be:

1) build bowtie2 index with bowtie2-build (bowtie2-build -f myFastaGenome myOutputBaseName)

2) align with botwie2 (bowtie2 -x myOutputBaseName -f myFastaFile -S mySamOutput)

3) index reference seq with samtools (samtools faidx myFastaGenome)

4) convert previous sam to bam (samtools -view -bS mySamOutput > myBamOutput)

5) the command line here

you need to find the A. lyrata reference genome, not sure if this helps.

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6.5 years ago
kirannbishwa01 ★ 1.3k

Thanks RS. I had read about this but I need something that has documentation and potentially already worked out examples to guide me through the process. Examples always help me understand the data better and helps with interpretation. I have been trying to work with BBmap but for right now I am trying to get it work first. I will see how it goes.

Thanks,

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