bwa的sampe和mem都可能会出现这个错误,当这个错误出现时,可能存在有以下原因: 1) fq1和fq2的reads名字不一致; 2)fq1和fq2对应reads的长度不一致; 3)fq1和fq2中的reads顺序不同 ......
samtools统计paired reads SAMtools是一个用于处理和分析基因组学中的序列数据的工具。它可以用于创建索引、比对、变异检测、基因组组装和其他相关任务。对于您提到的统计paired reads,SAMtools提供了一个名为idxstats的选项,它可以用于统计已比对到基因组的reads的数量和分布。 以下是使用SAMtools统计paired reads的步骤: ...
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问题: 在用BWA进行序列比对时出现:[mem_sam_pe] paired reads have different names: "A00920:973:H5GWJDSX3:2:1103:2582:12633:UMI_AAT_GTA", "A00920:973:H5GWJDSX3:2:1103:1624:12633:UMI... 问题: 在用BWA进行序列比对时出现:[mem_sam_pe] paired reads have different names: "A00920:973:H5...
Pevzner. De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Research, 19(2):336-346, 2009.Chaisson,M.J,Brinza,D,Pevzner,P.A.De novo fragment assembly with short mate-paired reads:does the read length matter?. Genome Research . 2009...
Illumina machine can generate paired reads where constructs are sequenced in both directions. When the forward and reverse reads overlap, they can be "assembled" or "merged" to give a single sequence. I prefer to call this merging rather than assembly to distinguish from whole-genome assembly us...
paired reads have different names: 001、问题bwa报错如下: paired reads have different names: 002、解决方法,对fastq文件的read名进行重命名 脚本如下: ## step1:处理 read1awk'END{tmp = NR / 4; split(FILENAME, a, "_"); for (i = 1; i <= tmp; i++) {print "@"a[1]"."i,i"/1"...
spark-submit --class SparkBWA \ --master yarn-client \ --conf "spark.executor.extraJavaOptions=-Djava.library.path=/home/hadoop/xubo/tools/SparkBWA/build" \ --archives ./bwa.zip \ SparkBWA.jar \ -algorithm mem -reads paired \ -index /home/hadoop/xubo/ref/GRCH38L1Index/GRCH38chr1L355...
-algorithm mem -reads paired \ -index /home/hadoop/xubo/ref/GRCH38L1Index/GRCH38chr1L3556522.fasta \ -partitions 3 \ /xubo/alignment/sparkBWA/GRCH38chr1L3556522N1000000L100paired1.fastq /xubo/alignment/sparkBWA/GRCH38chr1L3556522N1000000L100paired2.fastq \ ...
已有的方法是基于比对的策略来删除duplicates【2】,paired reads先是被比对上参考序列上,利用短序列比对工具(bowtie,crossbow,bwa),那些匹配的位置一模一样的就认为是duplicates,然后这些duplicates被这些工具给删掉(Rmdup in the SAMtools package [18], MarkDuplicates in the Picard toolkit [19], and SEAL).但是这...