Filtering sam or bam file with maximum matching region

Question

[analyst]

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

Answer 1

[Pierre Lindenbaum]

. 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;}'

[analyst]

Thanks Pierre!

I got this output

Can you please interpret the output

[Pierre Lindenbaum]

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),

[analyst]

Okay sure Pierre I will take care of it next time

[Pierre Lindenbaum]

the max depth is 3520 at chr1:80660513

[analyst]

Thanks for the interpretation Pierre!