search

rivas-lab / nanopore

Tools for analysis of long-read sequencing data.
0 stars 0 forks source link

throughput and quality of nanopore data #11

Closed yk-tanigawa closed 7 years ago

yk-tanigawa commented 7 years ago

Summary stats

cDNA WGS
Number of FAST5 files 48,280 184,911
total reads(*) 26,854 29,964
total base pairs 46,314,462 44,839,915
mean 1724.68 1496.46
median 1094 925
min 58 35
max 108262 94024
N25 5201 4547
N50 2529 2227
N75 1327 1140
# of seq (total) 26,854 92,186
# of seq > 1kb 14,550 42,572
# of seq > 10kb 302 660
# of seq > 20kb 21 102
yk-tanigawa commented 7 years ago

FastQC

cDNA

adapter_content duplication_levels kmer_profiles per_base_n_content per_base_quality per_base_sequence_content per_sequence_gc_content per_sequence_quality sequence_length_distribution 20161006_minion_human_cDNA_fastqc.zip

WGS

adapter_content duplication_levels kmer_profiles per_base_n_content per_base_quality per_base_sequence_content per_sequence_gc_content per_sequence_quality sequence_length_distribution 20161008_wgs_caucasian_48hr_fastqc.zip

yk-tanigawa commented 7 years ago

Quality assessment

-WGS data set seems to be T-rich.

yk-tanigawa commented 7 years ago