Report up to <int> alns per read; MAPQ not meaningful: Instead, it searches for at most <int> distinct, valid alignments for each read. The search terminates when it can't find more distinct valid alignments, or when it finds <int>, whichever happens first. All alignments found are repo...
--FILTERING_MAPQ 20 --FILTERING_DISCARD_SECONDARY true --FILTERING_PRIMARY_ALIGNMENTS true --FILTERING_OVERLAPPING_READS false --FILTERING_INTERVALS file:intervals.list --FILTERING_INTERVALS file:intervals.list input.bam是输入的SAM/BAM文件,output.bam是输出的SAM/BAM文件,其他选项可以根据需要进行设置。 4...
如果一个read来自重复区域,则可能map到多个地方,所以需要知道比对的可信程度。在SAM文件中,MAPQ就是这个,值为Q=-10log10p。p是对比对错误的概率的估计。一个read越特殊,比对错误的概率越小,Q值越大。 bowtie2是对paired read的每个mate分别比对的,所以如果两个比对结果不符合预期(比如方向不合适或者距离不合适),...
--score-min <func> min acceptable alignment score w/r/treadlength(G,20,8forlocal, L,-0.6,-0.6forend-to-end)Reporting:(default)lookformultiple alignments, report best, with MAPQ OR -k <int> report up to <int> alns per read;MAPQ not meaningful OR -a/--all report all alignments;very...
” To disable mixed mode, set the –no-mixed option. Bowtie 2 runs a little faster in –no-mixed mode, but will only consider alignment status of pairs per se, not individual mates. I.e. in SAM records for pairs, the optional YM:i flag will not appear and MAPQ values calculated ...
-q INT 跳过MAPQ(定位的质量)比INT小的序列[默认0] -l STR 只输出STR库中的序列 -r STR 只输出在STR读段组中的序列 2)samtoolsimport in.ref_list in.sam out.bam,从0.1.4起,它与samtools view‐bt in.ref_list‐o out.bam in.sam意义相同。 3)samtoolssort [‐n] [‐m maxMem] in.bam out...
Fix an issue causing Bowtie2 to set an incorrect MAPQ when AS and XS … Mar 25, 2021 util.h Fix compiler warning Dec 21, 2020 word_io.h Print a message and exit if readU and readI encounter short reads May 20, 2021 zbox.h Changed many data structures required to implement LFS. ...
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 4年前 zbox.h Changed many data structures required to implement LFS. 11年前 ...
1)samtoolsview[‐bhuHS] [‐t in.refList] [‐o output] [‐f reqFlag] [‐F skipFlag] [‐q minMapQ] [‐l library] [‐r read‐Group] in.bam|in.sam [region1 [...]],提取/打印所有的或者部分序列文件。如果没有指定区域,所有的序列都将会被打印。否则,仅仅打印覆盖特定区域的序列才会被打印...
(default) look for multiple alignments, report best, with MAPQ OR -k report up to alns per read; MAPQ not meaningful OR -a/--all report all alignments; very slow, MAPQ not meaningful Effort: -D give up extending after failed extends in a row (15) ...