高通量测序时,在芯片上的每个反应,会读出一条序列,是比较短的,叫read,它们是读序;就是我们测序产生的短读序列,通常一代和三代的reads读长在几千到几万bp之间,二代的相对较短,平均是几十到几百bp。PE reads 就是 paired-end reads。在测序过程中,一条DNA分子的两端都可以测序。先测其中的一端,获得一个re...
1、最初Sanger中心用Phred Quality Score来衡量该read中每个碱基的质量:Q=-10logP,其中P代表该碱基被测序错误的概率,如果该碱基测序出错的概率为0.001,则Q应该为30,那么30+33=63,那么63对应的ASCii码为“?”,则在该碱基对应的质量值即“?”。 2、Solexa系列测序仪使用不同的公示来计算质量值:Q=-10log(P/1...
C含量分布图 Per sequence GC content 这个图理论上应该符合正态分布(也就是钟形曲线),除非有过表达的序列( over-represented sequences)[也就是在正态分布的基础上有一个尖尖的峰],或者存在其他物种的污染[也就是多个峰] 从这个图中可以看到,这个应该是符合过表达序列的情况,说明要么存在序列污染,要么是有个特...
Add to fastp a per-sample barplot and a per-sequence table for the overrepresented seqeunces counts, similar to FastQC (though not entirely replicating). Fix #2997 Add overrpresented sequences plot and table 8561b9d vladsavelyev added the module: enhancement label Dec 5, 2024 vladsavelyev...
Haudry Y, Ramialison M, Paten B, Wittbrodt J, Ettwiller L. Using Trawler_standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation. Nat Protoc. 2010; 5 :323–334. [ PubMed ]...
Esther PT Lam1, Kwok-Yung Yuen1,2* Abstract Background: Out-of-frame stop codons (OSCs) occur naturally in coding sequences of all organisms, providing a mechanism of early termination of translation in incorrect reading frame so that the metabolic cost associated with frameshift events can be...
Esther PT Lam1, Kwok-Yung Yuen1,2* Abstract Background: Out-of-frame stop codons (OSCs) occur naturally in coding sequences of all organisms, providing a mechanism of early termination of translation in incorrect reading frame so that the metabolic cost associated with frameshift events can be...
Overrepresented k-mers in Upstream miRNA Sequences Are Preferentially Located towards the Genomic Loci of Protein-Coding GenesJi LeeZhihua LiRachel BrowerSinningBino John
CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequencesdoi:10.1186/1471-2105-13-32Yang DingWilliam Andrew LorenzJeffrey H. ChuangBioMed CentralDing, Y., Lorenz, W. A., and Chuang, J. H. (2012). CodingMotif: exact determination of overrepresented nucleotide motifs...
Overrepresented motifs in the piRNA (distinct) sequences of the A. gossypii libraries.Sampurna, SattarCharles, AddoQuayeYan, SongJames, A. AnsteadRamanjulu, SunkarGary, A. Thompson