QC On Raw Data
05 July, 2022
Last updated: 2022-07-05
Checks: 6 1
Knit directory:
20180328_Atkins_RatFracture/
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knitr::opts_chunk$set(
message = FALSE, warning = FALSE,
fig.height = 6, fig.width = 10
)library(ngsReports)
library(tidyverse)
library(yaml)
library(scales)
library(pander)
library(glue)
library(plotly)panderOptions("table.split.table", Inf)
panderOptions("big.mark", ",")
theme_set(theme_bw())
fh <- 6
suffix <- "_L001_R1.fastq.gz"
pattern <- paste0("_CB2YGANXX_.+fastq.gz")
sp <- "Rnorvegicus"samples <- "data/targets.csv" %>%
here::here() %>%
read_csv() %>%
mutate(
Filename = paste0(File, suffix)
)group_cols <- hcl.colors(
n = length(unique(samples$group)),
palette = "Zissou 1"
) %>%
setNames(unique(samples$group))Quality Assessment on Raw Data
rawFqc <- here::here("data/0_rawData/FastQC") %>%
list.files(pattern = "zip", full.names = TRUE) %>%
FastqcDataList() %>%
.[fqName(.) %in% samples$Filename]plotSummary(rawFqc, pattern = pattern)
Overall summary of FastQC reports
Library Sizes
A total of 6 libraries were contained in this dataset, with read totals ranging between 37,710,559 and 44,890,754 reads.
Across all libraries, reads were 100 bases.
plotReadTotals(rawFqc, pattern = pattern, usePlotly = TRUE)Library Sizes for all supplied fastq files. Any samples run as multiple libraries are shown as the supplied multiple libraries and have not been merged.
Sequence Quality
plotBaseQuals(
rawFqc,
pattern = pattern,
usePlotly = TRUE,
dendrogram = TRUE,
cluster = TRUE
)Mean sequencing quality scores at each base position for each library
GC Content
plotGcContent(
x = rawFqc,
pattern = pattern,
species = sp,
plotType = "line",
gcType = "Trans",
usePlotly = TRUE,
dendrogram = TRUE,
cluster = TRUE
)GC content shown as the % above and below the theoretical GC content for the Rnorvegicus transcriptome. The peaks at 62% and 71% are strongly suggestive of incomplete rRNA removal
Sequence Content
plotly::ggplotly(
getModule(rawFqc, module = "Per_base_sequence_content") %>%
mutate(Base = fct_inorder(Base)) %>%
group_by(Base) %>%
mutate(
across(c("A", "C", "G", "T"), function(x){x - mean(x)})
) %>%
pivot_longer(
cols = c("A", "C", "G", "T"),
names_to = "Nuc",
values_to = "resid"
) %>%
left_join(samples) %>%
ggplot(
aes(Base, resid, group = Filename, colour = group)
) +
geom_line() +
facet_wrap(~Nuc) +
scale_colour_manual(values = group_cols) +
labs(
x = "Read Position", y = "Residual", colour = "Group"
) +
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)
)
)Base and Position specific residuals for each sample. The mean base content at each position was calculated for each nucleotide, and the sample-specific residuals calculated.
AdapterContent
plotAdapterContent(
x = rawFqc,
pattern = pattern,
plotType = "line",
dendrogram = TRUE,
cluster = TRUE
) +
scale_y_continuous(expand = expansion(c(0, 0)), limits = c(0, 10))
Total Adapter Content for each sample shown by starting position in the read.
Overrepresented Sequences
os <- suppressMessages(getModule(rawFqc, "Over"))if (nrow(os)){
if (length(unique(os$Filename)) > 1){
suppressMessages(
plotOverrep(
x = rawFqc,
pattern = suffix,
usePlotly = TRUE,
dendrogram = TRUE,
cluster = TRUE
)
)
}
}Summary of over-represented sequences across all libraries
os %>%
group_by(Sequence, Possible_Source) %>%
summarise(
`Found in` = n(),
Total = sum(Count),
`Largest Percent` = glue("{round(max(Percentage), 2)}%")
) %>%
pander(
caption = "*Summary of over-represented sequences within the raw data. Manual checking of over-represented sequences using BLAST indicated most were Ribosomal in origin*"
)| Sequence | Possible_Source | Found in | Total | Largest Percent |
|---|---|---|---|---|
| ACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTC | No Hit | 1 | 45,817 | 0.1% |
| ACCAGGTCGATGCGTGGAGTGGACGGAGCAAGCTCCTATTCCAACTCCTA | No Hit | 6 | 1,602,565 | 1.18% |
| ACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGG | No Hit | 1 | 47,849 | 0.11% |
| ACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCCACGGGAAGG | No Hit | 1 | 65,603 | 0.15% |
| ACGACTTTTACTTCCTCTAGATAGTCAAGTTCGACCGTCTTCTCAGCGCT | No Hit | 1 | 65,230 | 0.15% |
| ACTCATTCCAATTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCG | No Hit | 1 | 99,858 | 0.22% |
| AGACGTTCGAATGGGTCGTCGCCGCCACGGAGGGCGTGCGATCGGCCCGA | No Hit | 1 | 76,924 | 0.17% |
| CACAGTTATCCAAGTAGGAGAGGAGCGAGCGACCAAAGGAACCATAACTG | No Hit | 2 | 230,166 | 0.26% |
| CACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACT | No Hit | 1 | 72,772 | 0.16% |
| CACCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCAT | No Hit | 6 | 824,551 | 0.52% |
| CACTACCACAAATTATGCAGTCGAGTTTCCCGCATTTGGGGAAATCGCAG | No Hit | 1 | 86,223 | 0.19% |
| CAGACGTTCGAATGGGTCGTCGCCGCCACGGAGGGCGTGCGATCGGCCCG | No Hit | 1 | 68,699 | 0.15% |
| CAGGTCGATGCGTGGAGTGGACGGAGCAAGCTCCTATTCCAACTCCTAGT | No Hit | 6 | 1,328,794 | 0.91% |
| CCACAGTTATCCAAGTAGGAGAGGAGCGAGCGACCAAAGGAACCATAACT | No Hit | 2 | 239,062 | 0.29% |
| CCACTACCACAAATTATGCAGTCGAGTTTCCCGCATTTGGGGAAATCGCA | No Hit | 1 | 98,089 | 0.22% |
| CCAGGTCGATGCGTGGAGTGGACGGAGCAAGCTCCTATTCCAACTCCTAG | No Hit | 3 | 414,384 | 0.39% |
| CCCACTACCACAAATTATGCAGTCGAGTTTCCCGCATTTGGGGAAATCGC | No Hit | 5 | 839,456 | 0.87% |
| CCCCACTACCACAAATTATGCAGTCGAGTTTCCCGCATTTGGGGAAATCG | No Hit | 5 | 1,131,951 | 1.18% |
| CCCCCACTACCACAAATTATGCAGTCGAGTTTCCCGCATTTGGGGAAATC | No Hit | 3 | 176,954 | 0.21% |
| CCCCGGCCGTCCCTCTTAATCATGGCCTCAGTTCCGAAAACCAACAAAAT | No Hit | 1 | 50,834 | 0.11% |
| CCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATAT | No Hit | 6 | 2,575,389 | 1.38% |
| CCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCG | No Hit | 2 | 294,754 | 0.54% |
| CCCGCACTTACTGGGAATTCCTCGTTCATGGGGAATAATTGCAATCCCCG | No Hit | 1 | 54,847 | 0.12% |
| CCCGCATTTGGGGAAATCGCAGGGGTCAGCACATCCGGAGTGCAATGGAT | No Hit | 1 | 64,491 | 0.14% |
| CCCGGAAGCTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAGT | No Hit | 2 | 147,329 | 0.2% |
| CCCGGCCGTCCCTCTTAATCATGGCCTCAGTTCCGAAAACCAACAAAATA | No Hit | 2 | 155,547 | 0.22% |
| CCCGGGGCCGCAAGTGCGTTCGAAGTGTCGATGATCAATGTGTCCTGCAA | No Hit | 3 | 181,978 | 0.18% |
| CCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG | No Hit | 1 | 81,033 | 0.18% |
| CCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTT | No Hit | 1 | 57,751 | 0.13% |
| CCCGTCGGCATGTATTAGCTCTAGAATTACCACAGTTATCCAAGTAGGAG | No Hit | 2 | 341,322 | 0.48% |
| CCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGG | No Hit | 3 | 210,456 | 0.23% |
| CCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATT | No Hit | 6 | 2,138,006 | 1.07% |
| CCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGG | No Hit | 1 | 108,328 | 0.24% |
| CCGGAAGCTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAGTC | No Hit | 1 | 76,694 | 0.17% |
| CCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCCACGGGAAGGG | No Hit | 2 | 128,537 | 0.19% |
| CCGTCGGCATGTATTAGCTCTAGAATTACCACAGTTATCCAAGTAGGAGA | No Hit | 2 | 212,925 | 0.29% |
| CCTCATTTGGATGTGTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCT | No Hit | 2 | 132,149 | 0.24% |
| CCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTG | No Hit | 6 | 1,244,652 | 0.59% |
| CCTCGTTCATGGGGAATAATTGCAATCCCCGATCCCCATCACGAATGGGG | No Hit | 1 | 53,902 | 0.12% |
| CCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCTTCGGGCCCCGCG | No Hit | 1 | 55,785 | 0.13% |
| CCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAAT | No Hit | 2 | 185,159 | 0.28% |
| CCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATG | No Hit | 6 | 1,363,560 | 0.76% |
| CCTTCCGTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCCCCCGG | No Hit | 1 | 76,012 | 0.17% |
| CGCCAGTCGGCATCGTTTATGGTCGGAACTACGACGGTATCTGATCGTCT | No Hit | 1 | 45,108 | 0.1% |
| CGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCC | No Hit | 2 | 211,183 | 0.31% |
| CGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCT | No Hit | 1 | 44,923 | 0.1% |
| CGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGAT | No Hit | 1 | 46,293 | 0.1% |
| CGCGTAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGAATTAACCA | No Hit | 1 | 101,017 | 0.23% |
| CGGGGAAGGTCGTCCTCTTCGACCGAGCGCGCAGCTTCGGGAGGGACGCA | No Hit | 1 | 81,803 | 0.22% |
| CGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCCACGGGAAGGGG | No Hit | 1 | 49,280 | 0.11% |
| CGTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCCCCCGGAACCC | No Hit | 2 | 105,954 | 0.13% |
| CGTCGGCATGTATTAGCTCTAGAATTACCACAGTTATCCAAGTAGGAGAG | No Hit | 2 | 180,218 | 0.27% |
| CTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGC | No Hit | 1 | 77,886 | 0.17% |
| CTCAGTTCCGAAAACCAACAAAATAGAACCGCGGTCCTATTCCATTATTC | No Hit | 1 | 66,580 | 0.15% |
| CTCATTCCAATTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGT | No Hit | 1 | 101,980 | 0.23% |
| CTCATTTGGATGTGTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTC | No Hit | 3 | 263,392 | 0.36% |
| CTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCAATTACA | No Hit | 1 | 61,149 | 0.14% |
| CTCCCATCCAAGTACTAACCAGGCCCGACCCTGCTTAGCTTCCGAGATCA | No Hit | 6 | 675,991 | 0.49% |
| CTCCGACTTTCGTTCTTGATTAATGAAAACATTCTTGGCAAATGCTTTCG | No Hit | 2 | 124,691 | 0.17% |
| CTCCGATTCTGCAATAGCAGGCTTGACCTGCCTTCACAACTGCATCTTGG | No Hit | 1 | 41,165 | 0.11% |
| CTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGC | No Hit | 1 | 60,565 | 0.14% |
| CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT | No Hit | 6 | 684,533 | 0.45% |
| CTCCTATTCCAACTCCTAGTTCCAAAAATCCATTTAATATATTGTCCTCG | No Hit | 4 | 230,458 | 0.17% |
| CTCCTCTATTCGGGGAAGGTCGTCCTCTTCGACCGAGCGCGCAGCTTCGG | No Hit | 3 | 154,373 | 0.14% |
| CTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGA | No Hit | 6 | 1,401,485 | 0.71% |
| CTCGCCACCAACATCATCAGGGTTCACCTTTCCCCACAGGCCATTAACAG | No Hit | 2 | 89,013 | 0.12% |
| CTCGTATACCCTTGACCGAAGACCGGTCCTCCTCTATTCGGGGAAGGTCG | No Hit | 1 | 49,929 | 0.11% |
| CTCGTTCATGGGGAATAATTGCAATCCCCGATCCCCATCACGAATGGGGT | No Hit | 1 | 88,581 | 0.2% |
| CTCGTTCGTTATCGGAATTAACCAGACAAATCGCTCCACCAACTAAGAAC | No Hit | 1 | 57,369 | 0.13% |
| CTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTA | No Hit | 1 | 61,916 | 0.14% |
| CTCTATTCGGGGAAGGTCGTCCTCTTCGACCGAGCGCGCAGCTTCGGGAG | No Hit | 1 | 45,048 | 0.1% |
| CTCTGGTCCGTCTTGCGCCGGTCCAAGAATTTCACCTCTAGCGGCGCAAT | No Hit | 1 | 129,334 | 0.29% |
| CTCTTAATCATGGCCTCAGTTCCGAAAACCAACAAAATAGAACCGCGGTC | No Hit | 3 | 443,318 | 0.57% |
| CTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGT | No Hit | 2 | 96,563 | 0.11% |
| CTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGA | No Hit | 2 | 218,958 | 0.33% |
| CTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAATGGACCTTG | No Hit | 5 | 1,176,836 | 1.08% |
| CTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATT | No Hit | 4 | 857,169 | 1.05% |
| CTTAATCATGGCCTCAGTTCCGAAAACCAACAAAATAGAACCGCGGTCCT | No Hit | 1 | 54,457 | 0.12% |
| CTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGC | No Hit | 6 | 386,884 | 0.23% |
| CTTCACCTTAGGGTTACCCATGATAGCAGAGGCAGAGGACAGGTCCCCAA | No Hit | 1 | 39,295 | 0.1% |
| CTTCCGTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCCCCCGGA | No Hit | 2 | 319,873 | 0.48% |
| CTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAAC | No Hit | 2 | 146,238 | 0.22% |
| CTTGATTAATGAAAACATTCTTGGCAAATGCTTTCGCTCTGGTCCGTCTT | No Hit | 1 | 164,171 | 0.37% |
| GCAGACGTTCGAATGGGTCGTCGCCGCCACGGAGGGCGTGCGATCGGCCC | No Hit | 1 | 79,199 | 0.18% |
| GCATCGTTTATGGTCGGAACTACGACGGTATCTGATCGTCTTCGAACCTC | No Hit | 1 | 54,697 | 0.12% |
| GCCAGAGTCTCGTTCGTTATCGGAATTAACCAGACAAATCGCTCCACCAA | No Hit | 1 | 56,084 | 0.12% |
| GCCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATA | No Hit | 1 | 40,199 | 0.11% |
| GCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCC | No Hit | 1 | 119,886 | 0.27% |
| GCCCTTCCGTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCCCCC | No Hit | 1 | 78,539 | 0.18% |
| GCCGGCTTCACGCTCAGGAGGGGACGCTATGTCTCGTCCTCGTGGTTTCG | No Hit | 1 | 43,693 | 0.11% |
| GCCTCAGTTCCGAAAACCAACAAAATAGAACCGCGGTCCTATTCCATTAT | No Hit | 2 | 172,403 | 0.23% |
| GCCTCATTTGGATGTGTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTC | No Hit | 1 | 74,957 | 0.2% |
| GCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCG | No Hit | 3 | 484,746 | 0.61% |
| GCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGA | No Hit | 2 | 127,409 | 0.19% |
| GCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTC | No Hit | 2 | 135,401 | 0.2% |
| GCGGTGTGTACAAAGGGCAGGGACTTAATCAACGCAAGCTTATGACCCGC | No Hit | 1 | 49,415 | 0.11% |
| GCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGG | No Hit | 1 | 49,062 | 0.11% |
| GCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGG | No Hit | 6 | 413,413 | 0.23% |
| GGACGCACATGGAGCGGTGAGGGAGGAAGGGGACACCCGCCTAGCCAGCC | No Hit | 2 | 99,505 | 0.15% |
| GGACTCATTCCAATTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTT | No Hit | 1 | 73,056 | 0.16% |
| GGAGGTTCTAGCAGGGGAGCGCAGCTACTCGTATACCCTTGACCGAAGAC | No Hit | 1 | 79,903 | 0.21% |
| GGCAGACGTTCGAATGGGTCGTCGCCGCCACGGAGGGCGTGCGATCGGCC | No Hit | 4 | 1,365,014 | 1.98% |
| GGCATCGTTTATGGTCGGAACTACGACGGTATCTGATCGTCTTCGAACCT | No Hit | 1 | 49,624 | 0.11% |
| GGCCTCAGTTCCGAAAACCAACAAAATAGAACCGCGGTCCTATTCCATTA | No Hit | 1 | 52,967 | 0.12% |
| GGCGGTGTGTACAAAGGGCAGGGACTTAATCAACGCAAGCTTATGACCCG | No Hit | 1 | 79,266 | 0.18% |
| GGGGAAGGTCGTCCTCTTCGACCGAGCGCGCAGCTTCGGGAGGGACGCAC | No Hit | 1 | 52,057 | 0.14% |
| GGGGCTTACATCAATGTGAGAGAAGTAGGTCTTGGTGGTGGGGAAGGCAG | No Hit | 1 | 39,514 | 0.1% |
| GGGGGGTCAGCGCCCGTCGGCATGTATTAGCTCTAGAATTACCACAGTTA | No Hit | 2 | 207,892 | 0.27% |
| GGGGGTCAGCGCCCGTCGGCATGTATTAGCTCTAGAATTACCACAGTTAT | No Hit | 1 | 52,050 | 0.12% |
| GGGGTCAGCGCCCGTCGGCATGTATTAGCTCTAGAATTACCACAGTTATC | No Hit | 2 | 113,824 | 0.13% |
| GGGTCGATGCGTGGAGTGGACGGAGCAAGCTCCTATTCCAACTCCTAGTT | No Hit | 1 | 52,061 | 0.14% |
| GGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGAATTA | No Hit | 1 | 68,510 | 0.15% |
| GGTCGATGCGTGGAGTGGACGGAGCAAGCTCCTATTCCAACTCCTAGTTC | No Hit | 6 | 1,539,951 | 1.09% |
| GGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCC | No Hit | 1 | 47,955 | 0.11% |
| GTACAAAGGGCAGGGACTTAATCAACGCAAGCTTATGACCCGCACTTACT | No Hit | 1 | 80,575 | 0.18% |
| GTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTG | No Hit | 1 | 65,065 | 0.15% |
| GTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCCCCCGGAACCCA | No Hit | 2 | 109,533 | 0.12% |
| GTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTT | No Hit | 1 | 69,064 | 0.15% |
| GTCCCCCACTACCACAAATTATGCAGTCGAGTTTCCCGCATTTGGGGAAA | No Hit | 4 | 472,827 | 0.46% |
| GTCCCTCTTAATCATGGCCTCAGTTCCGAAAACCAACAAAATAGAACCGC | No Hit | 2 | 167,043 | 0.24% |
| GTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTA | No Hit | 4 | 612,866 | 0.66% |
| GTCGATGCGTGGAGTGGACGGAGCAAGCTCCTATTCCAACTCCTAGTTCC | No Hit | 6 | 1,390,188 | 0.95% |
| GTCGCGTAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGAATTAAC | No Hit | 1 | 174,882 | 0.39% |
| GTCGGCATCGTTTATGGTCGGAACTACGACGGTATCTGATCGTCTTCGAA | No Hit | 1 | 61,947 | 0.14% |
| GTCGGCATGTATTAGCTCTAGAATTACCACAGTTATCCAAGTAGGAGAGG | No Hit | 4 | 877,632 | 1% |
| GTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAATGGACCT | No Hit | 5 | 805,129 | 0.76% |
| GTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCCC | No Hit | 2 | 206,070 | 0.31% |
| GTGCGATCGGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGA | No Hit | 1 | 50,483 | 0.11% |
| GTGGACTCATTCCAATTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTT | No Hit | 1 | 57,242 | 0.13% |
| GTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGA | No Hit | 2 | 139,349 | 0.22% |
| GTGTGTACAAAGGGCAGGGACTTAATCAACGCAAGCTTATGACCCGCACT | No Hit | 1 | 73,383 | 0.16% |
| GTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGC | No Hit | 1 | 46,188 | 0.1% |
| GTTCGAAGTGTCGATGATCAATGTGTCCTGCAATTCACATTAATTCTCGC | No Hit | 1 | 57,777 | 0.13% |
| GTTCGTTATCGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGC | No Hit | 1 | 84,329 | 0.19% |
| GTTCTTGATTAATGAAAACATTCTTGGCAAATGCTTTCGCTCTGGTCCGT | No Hit | 1 | 77,063 | 0.17% |
| GTTGGTTTTGATCTGATAAATGCACGCATCCCCCCCACGGGAAGGGGGGT | No Hit | 2 | 174,018 | 0.2% |
| TCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGAT | No Hit | 3 | 158,106 | 0.14% |
| TCTTAATCATGGCCTCAGTTCCGAAAACCAACAAAATAGAACCGCGGTCC | No Hit | 1 | 58,599 | 0.13% |
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
locale: LC_CTYPE=en_AU.UTF-8, LC_NUMERIC=C, LC_TIME=en_AU.UTF-8, LC_COLLATE=en_AU.UTF-8, LC_MONETARY=en_AU.UTF-8, LC_MESSAGES=en_AU.UTF-8, LC_PAPER=en_AU.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_AU.UTF-8 and LC_IDENTIFICATION=C
attached base packages: stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: plotly(v.4.10.0), glue(v.1.6.2), pander(v.0.6.5), scales(v.1.2.0), yaml(v.2.3.5), forcats(v.0.5.1), stringr(v.1.4.0), dplyr(v.1.0.9), purrr(v.0.3.4), readr(v.2.1.2), tidyr(v.1.2.0), tidyverse(v.1.3.1), ngsReports(v.1.13.0), tibble(v.3.1.7), ggplot2(v.3.3.6), BiocGenerics(v.0.42.0) and workflowr(v.1.7.0)
loaded via a namespace (and not attached): bitops(v.1.0-7), fs(v.1.5.2), bit64(v.4.0.5), lubridate(v.1.8.0), RColorBrewer(v.1.1-3), httr(v.1.4.3), rprojroot(v.2.0.3), GenomeInfoDb(v.1.32.1), tools(v.4.2.0), backports(v.1.4.1), bslib(v.0.3.1), utf8(v.1.2.2), R6(v.2.5.1), DT(v.0.22), DBI(v.1.1.2), lazyeval(v.0.2.2), colorspace(v.2.0-3), withr(v.2.5.0), tidyselect(v.1.1.2), processx(v.3.5.3), bit(v.4.0.4), compiler(v.4.2.0), git2r(v.0.30.1), rvest(v.1.0.2), cli(v.3.3.0), xml2(v.1.3.3), ggdendro(v.0.1.23), labeling(v.0.4.2), sass(v.0.4.1), callr(v.3.7.0), digest(v.0.6.29), rmarkdown(v.2.14), XVector(v.0.36.0), pkgconfig(v.2.0.3), htmltools(v.0.5.2), highr(v.0.9), dbplyr(v.2.1.1), fastmap(v.1.1.0), htmlwidgets(v.1.5.4), rlang(v.1.0.2), readxl(v.1.4.0), rstudioapi(v.0.13), farver(v.2.1.0), jquerylib(v.0.1.4), generics(v.0.1.2), zoo(v.1.8-10), jsonlite(v.1.8.0), crosstalk(v.1.2.0), vroom(v.1.5.7), RCurl(v.1.98-1.6), magrittr(v.2.0.3), GenomeInfoDbData(v.1.2.8), Rcpp(v.1.0.8.3), munsell(v.0.5.0), S4Vectors(v.0.34.0), fansi(v.1.0.3), lifecycle(v.1.0.1), stringi(v.1.7.6), whisker(v.0.4), MASS(v.7.3-57), zlibbioc(v.1.42.0), plyr(v.1.8.7), grid(v.4.2.0), parallel(v.4.2.0), promises(v.1.2.0.1), crayon(v.1.5.1), lattice(v.0.20-45), Biostrings(v.2.64.0), haven(v.2.5.0), hms(v.1.1.1), knitr(v.1.39), ps(v.1.7.0), pillar(v.1.7.0), reshape2(v.1.4.4), stats4(v.4.2.0), reprex(v.2.0.1), evaluate(v.0.15), getPass(v.0.2-2), data.table(v.1.14.2), modelr(v.0.1.8), vctrs(v.0.4.1), tzdb(v.0.3.0), httpuv(v.1.6.5), cellranger(v.1.1.0), gtable(v.0.3.0), assertthat(v.0.2.1), xfun(v.0.30), broom(v.0.8.0), later(v.1.3.0), viridisLite(v.0.4.0), IRanges(v.2.30.0), ellipsis(v.0.3.2) and here(v.1.0.1)
sessionInfo()R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] plotly_4.10.0 glue_1.6.2 pander_0.6.5
[4] scales_1.2.0 yaml_2.3.5 forcats_0.5.1
[7] stringr_1.4.0 dplyr_1.0.9 purrr_0.3.4
[10] readr_2.1.2 tidyr_1.2.0 tidyverse_1.3.1
[13] ngsReports_1.13.0 tibble_3.1.7 ggplot2_3.3.6
[16] BiocGenerics_0.42.0 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] bitops_1.0-7 fs_1.5.2 bit64_4.0.5
[4] lubridate_1.8.0 RColorBrewer_1.1-3 httr_1.4.3
[7] rprojroot_2.0.3 GenomeInfoDb_1.32.1 tools_4.2.0
[10] backports_1.4.1 bslib_0.3.1 utf8_1.2.2
[13] R6_2.5.1 DT_0.22 DBI_1.1.2
[16] lazyeval_0.2.2 colorspace_2.0-3 withr_2.5.0
[19] tidyselect_1.1.2 processx_3.5.3 bit_4.0.4
[22] compiler_4.2.0 git2r_0.30.1 rvest_1.0.2
[25] cli_3.3.0 xml2_1.3.3 ggdendro_0.1.23
[28] labeling_0.4.2 sass_0.4.1 callr_3.7.0
[31] digest_0.6.29 rmarkdown_2.14 XVector_0.36.0
[34] pkgconfig_2.0.3 htmltools_0.5.2 highr_0.9
[37] dbplyr_2.1.1 fastmap_1.1.0 htmlwidgets_1.5.4
[40] rlang_1.0.2 readxl_1.4.0 rstudioapi_0.13
[43] farver_2.1.0 jquerylib_0.1.4 generics_0.1.2
[46] zoo_1.8-10 jsonlite_1.8.0 crosstalk_1.2.0
[49] vroom_1.5.7 RCurl_1.98-1.6 magrittr_2.0.3
[52] GenomeInfoDbData_1.2.8 Rcpp_1.0.8.3 munsell_0.5.0
[55] S4Vectors_0.34.0 fansi_1.0.3 lifecycle_1.0.1
[58] stringi_1.7.6 whisker_0.4 MASS_7.3-57
[61] zlibbioc_1.42.0 plyr_1.8.7 grid_4.2.0
[64] parallel_4.2.0 promises_1.2.0.1 crayon_1.5.1
[67] lattice_0.20-45 Biostrings_2.64.0 haven_2.5.0
[70] hms_1.1.1 knitr_1.39 ps_1.7.0
[73] pillar_1.7.0 reshape2_1.4.4 stats4_4.2.0
[76] reprex_2.0.1 evaluate_0.15 getPass_0.2-2
[79] data.table_1.14.2 modelr_0.1.8 vctrs_0.4.1
[82] tzdb_0.3.0 httpuv_1.6.5 cellranger_1.1.0
[85] gtable_0.3.0 assertthat_0.2.1 xfun_0.30
[88] broom_0.8.0 later_1.3.0 viridisLite_0.4.0
[91] IRanges_2.30.0 ellipsis_0.3.2 here_1.0.1