Computational Systems Biology Methods and Protocols.7z
BWA-MEM. BWA-MEM is generally recommended for high- quality queries, as it is faster and more accurate. But be aware that BWA an ...
low-frequency mutations but likely to report a large amount of false-positive mutations. So we could not find a perfect variant ...
The authors have created an open source project to demon- strate this pipeline, which is available at GitHub (https://github. co ...
Since cfDNA fragments are usually short (~167 bp) [9], 2 150 paired-end sequencing will result in overlapped read pairs. Based ...
has some drawbacks. The first drawback is that local trimming only uses the quality information for trimming, but it cannot util ...
ed.(R 1 o1,R 2 o1)>ed.(R 1 o,R 2 o)<ed.(R 1 o+1,R 2 o+ 1). Figure4 shows an example of how AfterQC’s overlapping analysi ...
NNNRNYNN), or defined nucleotides (when template molecules are limited). UID or UMI could be introduced to targeted tem- plates ...
for Illumina TrueSeq). UID extraction is much easier in this case since it can be taken directly from the sample index. This pro ...
The baseline should store each mutation with its chromosome, position, reference, and alternative bases, combined with numbers o ...
visualize and validate target mutations. Figure5 shows a demon- stration of MutScan’s interactive mutation pileup. MutScan is av ...
FusionDirect needs a BED file containing four columns (chro- mosome, start position, end position, gene name). If this file is n ...
There exist some tools to remove PCR duplication. Picard MarkDuplicates compares sequences in the five primary positions of both ...
MrBam will give numbers of unique reads for a combination of following conditions: supporting reference or alternative, clustere ...
fragments, and methylated adapters are ligated to the DNA frag- ments. The DNA fragments are size-selected before sodium bisul- ...
The QA process for BS-seq data is like the same process for normal sequencing data, including quality profiling, adapter trimmin ...
researchers. We cannot discuss all the aspects of BS-seq in this chapter. A collection of BS-seq data analysis tools and pipelin ...
sequenced, and the normal sample can be used as a reference to determine the mutations called in tumor sample to be germline or ...
SeqMaker is a tool which generates sequencing reads with SNV, INDEL, CNV, and gene fusion enabled, with sequencing error and PCR ...
Since ctDNA should be sequenced very deeply, typically target capturing with small gene panels is applied with cost consideratio ...
Another topic that remains to be discussed is CNV detection. Since tumor-specific DNA is only a small part of cfDNA, copy number ...
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