IGV (Integrative Genome Viewer) Software Tutorial | Howto visualize bam files | Episode 1

[@muhammadakmal1414]

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?

[@minerva5435]

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.

[@thelion9489]

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.

[@bioinformaticscforbeginners]

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

[@thelion9489]

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

[@rufus9322]

Thank you

[@bioinformaticscforbeginners]

You have to index your bam file
samtools index bamfile

[@TashaTolefree-r8n]

Cornell Hill

[@FieldingBeck]

37034 Windler Forges

[@TroyNorman-u9d]

Leslie Fields

[@DrydenBrady]

640 Olga Corners

[@BertramMeroy-h3w]

Collin Port

[@DaltonAllen-k1u]

Bartoletti Parkways

[@EdisonMurphy-t1i]

Roob Spring

[@TracyAugust-c1s]

Warren Meadows

[@AnnRios-b9s]

Diego Fall

[@GerriGeary-g6n]

Green Park

[@YulandaLetteney-i4k]

Langosh Highway

[@KatharineElectra-k2d]

Ryan Landing

[@HaywoodMorton-m8v]

Dereck Shores

[@SonyaFerris-b9b]

DuBuque Place

[@RandalHintzen-x9h]

Okey Center

[@BarbaraGarcia-z4x]

Jewel Rapid

[@WoolleyLucius-q3n]

Bailey Summit

[@LattimoreNigel-g4s]

Sammy Pike

[@NoraKelly-f6q]

Crona Point

[@BenedictKyle-v7t]

Makayla Motorway

[@MonicaKehoe-t3t]

Treva Union

[@GabrielEady-v4f]

Duane Rapid

[@TomScaff-g4e]

King Mews

[@AnthonyHall-k8p]

Rohan Dale

[@LouisRoberts-q7w]

Cummerata Islands

[@TaylorSullins-l4c]

Mazie Green

[@MarionRadle-i1n]

Schoen Neck

[@MinnieBennett-e3n]

557 Murazik Light

[@LavoniaNanik-q5u]

Miguel Land

[@GeorgeBartholomew-z7v]

Metz Spur