I have assembled a genome and later re-organised ( reverse compliment and/or re-arrange some base) to make it collinear with its closet one relative. which file one should upload as reference sequence to determine the sequencing depth/coverage dips and low coverage areas? initially assembled genome or re-arranged one?

hi :) thank you for the video. i did not understand the coverage levels. the higher level coverages have a lots of blank parts above. but shouldn't those with blanks have a lower coverage than those without? because the blank-free regions have more fragment than others.

Thank you

@bioinformaticsclips

Жыл бұрын

You have to index your bam file samtools index bamfile

Thanks for this vedio. Can you please help me with my case, I have two bam file T2T has been done for them both, and now i want to extract shared SNP between our files. I have IGV but i am struggling in how to find shared SNP.

@bioinformaticsclips

Жыл бұрын

I will suggest you call the snps first (using tools like bcftools, gatk,etc). And then you can do the comparison

@thelion9489

Жыл бұрын

Can you please send me a link sir for those a.Thanks for your help. @@bioinformaticsclips