理解soft-clipped reads 什么是soft-clipped reads 当基因组发生某一段的缺失,或转录组的剪接,在测序过程中,横跨缺失位点及剪接位点的reads回帖到基因组时,一条reads被切成两段,匹配到不同的区域,这样的reads叫做soft-clipped reads,这些reads对于鉴定染色体结构变异及外源序列整合具有重要作用。 什么是multi-hits reads...
I am looking at whole genome sequencing DNA data and interested in insertions such as LINE1 retrotransposons or viruses. I would like to have a way to get rid of all of the reads which do not have soft-clipped segments, to be left with o...
side; read depth information for CNV: DO=read depth outside, DI=read depth inside, D1=read depth on 1st break point, D2=on the second; paired-end information: PR=number of pairs that enclose the CNV; KM=length of kmers for the matched reads; Q0=percentage of ambiguous q=0 reads....
那么,HDFS层面也有它自己的优化点,即:Short-Circuit Local Reads。本篇博客笔者将从HDFS层面来进行优化,从而间接的提升HBase... cxhfuujust 0 359 SOFT-NMS (二) (non maximum suppression,非极大值抑制) 2019-09-30 16:32 − import numpy as npboxes = np.array([[200, 200, 400, 400], [...
Thanks for the rapid response, Jim. Re window - yes thats what I meant. I've attached an example - it's not the best example but its the best I could get right now. In this example there are several examples of reads where every base in the current window is soft clipped (the 1st...
Filter SAM file for soft and hard clipped alignments Introduction Most short read aligners perform local alignment of reads to the reference genome. Examples includes bwa mem, minimap2, and bowtie2 (unless in --end-to-end mode). This means the ends of the read may not be part of the ...