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This note based blog covers bioinformatics and cancer genomics

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DNA fragment size, insert size and pre-merging

During the standard library preparation, we usually use physical or enzymatic methods to fragment DNA. How different fragment size affects downstream analysis and how do we choose optimal fragment size? Generally speaking, the optimal fragment size depends on the goal of analysis, the region of interest and sequencing technique. Let's split fragment size to three scenario and discuss them separately. Fragment longer than 2*read length Longer DNA fragment creates an insert reg

CNV detection in capture based sequencing

CNV detection in capture based sequencing

Copy number variations (CNVs) have been well studied regarding their association with tumorigenesis. Meanwhile, numerous targeted therapies have been approved to target specific CNV harbored in the tumor cells. Here we talk about some basics of CNV and its detection. It is believed that CNV promote tumorigenesis by altering the expression of oncogene and tumor suppressor. For example, the amplification of oncogene or deletion of tumor suppressor. It is interesting to note tha

A few elusive information in BAM / SAM format

A few elusive information in BAM / SAM format

bam file may store more alignment information than you think. As probably the most important format in NGS analysis, almost all sorts of variants are identified from it. It is critical that we get a full image of bam format. Here I like to mention some of the subtle tags in bam format. They may seems less critical than others. These info have been super useful for certain customized analysis or in times of retrospective check. M in CIGAR, NM tag and MD tag CIGAR shows matchin

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