3. Introduction to Data Preprocessing

[@NIPTMED]

Bowtie2. I use it for aligment with reference before I call variant by GATK ?

[@nikitamaurya4518]

love this!

[@edoardoabeni6450]

At 9:17 the speaker did not finish to explain why there are 2 matches!

[@dawei6697]

Horrible speakers struggling with drawing complete sentences.... she only explained what the 2 matches are NOT, but murmured through what they really are..”match the positions in the reference genome”? Hello? Base matches positions? Orange matches Apple?

[@ChipsterTutorials]

This is a recording of a live lecture -the audience members are asking some questions in between, which are unfortunately not completely audible. The lecturer continues to explain the same issue with the 3M in the beginning of the read: the message is that it is checked whether the bases positions align, regardless if they are mismatches or matches. So insertions and deletions are sort of the beef here. Here's for example a nice text explaining the CIGAR: sites.google.com/site/bioinformaticsremarks/bioinfo/sam-bam-format/what-is-a-cigar

[@changfengchen9250]

What if there happen to be two independent reads that have the same 5' and 3' ends?

[@ChipsterTutorials]

Assuming this is regarding duplicate marking, here's a nice documentation regarding MarkDuplicates function: gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-