所以我们先用grep “AS:” aligned.sam将所有比对上的reads提取出来。 XS:i:<N>: Alignment score for the best-scoring alignment found other than the alignment reported. Can be negative. Can be greater than 0 in [--local] mode (but not in [--end-to-end]mode). Only present if the SAM ...
之前一贯使用的是BWA,根据文献描述,BWA速度比较慢但是比较精确,Bowtie比较快消耗的内存也比较小。目前用自己的8G笔记本,使用Bowtie比对二代测序reads到人类基因组上,的确是可以跑得开的。 首先,先区别一下这些大名鼎鼎的比对软件。 TopHat: a fastsplice junction mapperforRNA-seq reads Cufflinks: a tool fortran...
· XS:i 第二好的匹配的得分 · YS:i mate 序列匹配的得分 · XN:i 在参考序列上模糊碱基的个数 · XM:i 错配的个数 · XO:i gap open的个数 · XG:i gap 延伸的个数 · NM:i 经过编辑的序列 · YF:i 说明为什么这个序列被过滤的字符串 · YT:Z · MD:Z 代表序列和参考序列错配的字符串...
1 (100.00%)wereunpaired;ofthese: 0 (0.00%)aligned0times0 (0.00%)alignedexactly1time1 (100.00%)aligned>1times0 16chr15101979467 1 50M* 0 0GACCAAACAGCATATGCTCCGGGTGTTTCCCTATAATCCGCCAGTACTGTIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIAS:i:0XS:i:0XN:i:0XM:i:0XO:i:0XG:i:0NM:...
XS:i:<N> Alignment score for second-best alignment.当Align>1 time出现 YS:i:<N> Alignment score for opposite matein the paired-end alignment.当该read是双末端测序中的一条时出现 XN:i:<N> The number of ambiguous bases in the reference covering this alignment.(推测是指不知道错配发生在哪个位...
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Information about the best alignments is used to estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. When -k is specified, however, bowtie2 behaves differently. Instead, it searches for at most <int> distinct, valid alignments for each read. The search ...
Hi, it would be great if Bowtie 2 could move fastq read header comments to sam tags, similar to the "-C" function of BWA MEM. Although Bowtie 2 supports alignment of ubams (unlike BWA), which would preserve tags that already exist, unfor...
o.append("XS:i:"); o.append(buf); } else { // If we did not find a secondary alignment for the read and // the average seed hits is less than the max DP failures allowed, // then we conclude that the alignment is unique. int mate = (rd.mate < 2 ? 0 : 1); ...
Fix an issue causing Bowtie2 to set an incorrect MAPQ when AS and XS a… 4年前 util.h Fix compiler warning 4年前 word_io.h Print a message and exit if readU and readI encounter short reads 3年前 zbox.h Changed many data structures required to implement LFS. 11年前 ...