AI代码解释 ## 进行 reads 比对STAR--twopassMode Basic \--quantMode TranscriptomeSAM GeneCounts \--runThreadN6\--genomeDir index_dir \--alignIntronMin20\--alignIntronMax50000\--outSAMtypeBAMSortedByCoordinate \--sjdbOverhang149\--outSAMattrRGlineID:sampleSM:samplePL:ILLUMINA\--outFilterMismatch...
star的twopassMode问题 如果只有一个样本,那么通常推荐加上这个--twopassModeBasic参数,可以保证更精准的比对情况,也方便去找变异,其官方文档解释如下: Annotated junctions will be included in both the 1st and 2nd passes. To run STAR 2-pass mapping for each sample separately,use --twopassMode Basic opt...
STAR --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --runThreadN 6 --genomeDir index_dir --alignIntronMin 20 --alignIntronMax 50000 --outSAMtype BAM SortedByCoordinate --sjdbOverhang 149 --outSAMattrRGline ID:sample SM:sample PL:ILLUMINA --outFilterMismatchNmax 2 --outSJfilter...
--outFileNamePrefix ./SRR3589959_2-pass 上述方法original方法适用于多样本和单个样本的处理,但是如果是per-sample(单个样本?)的2-pass mapping,可以直接用--twopassMode Basic参数将第两步mapping中的make index省去,直接再mapping STAR --runThreadN 20 --genomeDir ~/reference/index/STAR/mm10/ \ --two...
对于单个样本,在比对时直接添加--twopassMode Basic参数,软件会自动进行两次比对,将第一次比对的SJ.out.tab加入到索引,然后重新比对。这种方法操作简单,适用于单个样本的2-pass 比对。 更多参数和用法请参考官方文档。 ·end· ...
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STAR --runThreadN 20 --genomeDir ~/reference/index/STAR/mm10/ \ --twopassMode Basic \ --readFilesIn SRR3589959_1.fastq SRR3589959_2.fastq \ --outSAMtype BAM SortedByCoordinate \ --outFileNamePrefix ./SRR3589959 这个比常规的结果还多2个临时产生的文件夹(SRR3589959_STARgenome,SRR358995...