Shorter split hits
bwa mem 比对时，会有一个 -M 参数，bwa官方给出的解释是 mark shorter split hits as secondary。-M 参数用来处理同一个reads比对到参考基因组上不同位置的情况。 不加 -M. 目前的比对，都不加 -M. 如果不加入 -M 参数，这种情况bam中的 flag= 2048 ( supplementary alignment ) Prikaži več Splet17. mar. 2024 · 有些软件如 Picard’s markDuplicates 跟 mem 的这种剪接性比对不兼容,在这种情况下，可以使用 –M 选项来将 shorter split hits 标记为次优。 常用参数：-t 线程 …
Shorter split hits
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SpletWhy should mark shorter split hits as secondary ?solution Characterize the fragment size distribution Before we can attempt to identify structural variants via discordant … Splet24. maj 2016 · -M 将 shorter split hits 标记为次优，以兼容 Picard’s markDuplicates 软件。-p 若无此参数：输入文件只有 1 个，则进行单端比对；若输入文件有 2 个，则作为paired …
SpletI did use the –M option (Mark Shorter Split Hits as Secondary). Here are the steps I took: 1) FASTQ Groomer on both Fastq Files. 2) BWA-MEM with groomed FASTQ’s (-M) 3) Addorreplacereadgroups. 4) Clean Sam (on .BAM file) 4) Paired read mate fixer. 5) MarkDuplicate Reads (Failed) Splet12. apr. 2024 · The formation that originally consisted of 8,400 men was split into two legions of 4,200 men each, destined to a different form of combat. The staff which could be defmed as the main weapon of the ...
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