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Filtering sam or bam file with maximum matching region

Hi all,

I am analysing NGS amplicon reads of crisper gene samples. I do not know exactly which genes do they belong to because if I align reads against gene sequence (that was supposed to be) using BWA it gives 0% identity however by aligning reference genome I get 99% alignment rate. Now how can I find about the gene through reads data. Is there any way to find through sam or bam file that which chromosomal position are maximum reads aligning to?

Thanks

crisper-edited alignment match
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written by Bushra Bibi Bushra Bibi

1 answer

. Is there any way to find through sam or bam file that which chromosomal position are maximum reads aligning to?

samtools depth in.bam | awk -F '\t' 'BEGIN{BEST_DEPTH=0;BEST="";} {DEPTH=int($3);if(BEST_DEPTH<DEPTH) {BEST_DEPTH=DEPTH;BEST=$0;} } END{print BEST;}'
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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks Pierre!

I got this output

Can you please interpret the output

enter image description here

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written by Bushra Bibi Bushra Bibi

Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below),

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written by Pierre Lindenbaum Pierre Lindenbaum

Okay sure Pierre I will take care of it next time

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written by Bushra Bibi Bushra Bibi

Thanks for the interpretation Pierre!

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written by Bushra Bibi Bushra Bibi

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