Authoring Books with R Markdown
1 Saccharomyces cerevisiae dataset
2 NGS Pipeline: Saccharomyces cerevisiae samples
3 input reads and output
4 Phred offset
5 thresholds for mapping
6 unique mapping and multi-mapping
7 indel detection
8 read trimming
9 distance and orientation of paired end reads
10 number of CPU threads
11 read group
12 read order
13 color space reads
14 dynamic programming
15 detect structural variants
16 gene annotation
17 others
18 Multi-mapping reads
19 Fractional counting
20 Learning the BAM format
21 RNAseq diferential & exploratory analysis
22 Data Wrangling and Analyses with Tidyverse”
23 Data visualization with ggplot2
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RNA-genomics

4 Phred offset

-P <3:6> Offset value added to the Phred quality score of each read base. ‘3’ for phred+33 and ‘6’ for phred+64. ‘3’ by default.