uniquely mapped reads number - EAS

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  1. 5897884
    UNIQUE READS: Uniquely mapped reads number | 5897884 Uniquely mapped reads % | 82.49% Average mapped length | 200.55

    Uniquely mapped reads % very low · Issue #1571 · alexdobin/STAR

    github.com/alexdobin/STAR/issues/1571
    github.com/alexdobin/STAR/issues/1571
    這對您是否有幫助?
  2. 大家還會問
    How to get uniquelly mapped reads?
    Getting uniquelly mapped reads requires familiarity with SAM format, alignment flags, interpreting alignment types and Phread-scaled MAPQ, etc. These are some of useful discussion posts to go through before extracting reads mapped uniquely or at multiple sites. The Phred quality score (Q) is logarithmically related to the error probability (E).

    get uniquely mapped reads vs reads mapped at multiple sites from ... - …

    gist.github.com/sbamin/27acf13f2a28161efbf89a273559…
    搜尋: How to get uniquelly mapped reads?
    How many reads are mapped with Star?
    Reads: Input : 10206806 Mapped : 10058745 (98.5% of input) of these: 347302 ( 3.5%) have multiple alignments (2093 have >20) 98.5% overall read mapping rate. My STAR parameters are pretty much default. Do you know how I could acquire more uniquely aligned reads with STAR?

    Less multimapping reads, more uniquely mapped reads

    github.com/alexdobin/STAR/issues/215
    搜尋: How many reads are mapped with Star?
    How many reads are mapped with starindex?
    Reads: Input : 10206806 Mapped : 10058745 (98.5% of input) of these: 347302 ( 3.5%) have multiple alignments (2093 have >20) 98.5% overall read mapping rate. My STAR parameters are pretty much default. Do you know how I could acquire more uniquely aligned reads with STAR? Can STARindex have something to do with this:

    Less multimapping reads, more uniquely mapped reads

    github.com/alexdobin/STAR/issues/215
    搜尋: How many reads are mapped with starindex?
    How to exclude all possible multi-mapped reads from a BWA-mapped BAM file?
    To exclude all possible multi-mapped reads from a BWA-mapped BAM file, it looks like you need to use grep on the uncompressed SAM fields: samtools view -h mapped.bam | grep -v -e 'XA:Z:' -e 'SA:Z:' | samtools view -b > unique_mapped.bam Explanation follows...

    Obtaining uniquely mapped reads from BWA mem alignment

    bioinformatics.stackexchange.com/questions/508/obtaini…
    搜尋: How to exclude all possible multi-mapped reads from a BWA-mapped BAM file?
    意見反應

  3. Uniquely mapped reads number - Google Groups

    https://groups.google.com/g/rna-star/c/ipHc9FrgaPU

    2016年5月4日 · Mapping speed, Million of reads per hour | 82.82 Number of input reads | 65014569 Average input read length | 287 UNIQUE READS: Uniquely mapped reads number | 59712033 Uniquely mapped reads % |...

  4. unique mapped reads_weixin_34319111的博客-CSDN博客

    https://blog.csdn.net/weixin_34319111/article/details/86395320

    2017年1月9日 · 就是指唯一比对的reads. 现在人们已经开始避免使用unique mapped reads这个概念了，而转向使用mapq值来保留高质量的比对结果。. 因为mapq值反应了一组比对结果发生 …

  5. Get the "Uniquely mapped reads number" from BAM file #1535

    https://github.com/alexdobin/STAR/issues/1535

    Is there a way with samtools or another tool to get the "Uniquely mapped reads number" of the .Log.final.out file from just the BAM file? I have already tried converting BAM to FASTQ and …

  6. Obtaining uniquely mapped reads from BWA mem …

    https://bioinformatics.stackexchange.com/questions/508

    2017年6月7日 · The concept of "uniquely mapped reads" is a loaded term, and most sources suggest filtering by MAPQ should do the trick. However, this approach doesn't seem to work …

  7. Uniquely mapped reads % very low · Issue #1571 · alexdobin/STAR

    https://github.com/alexdobin/STAR/issues/1571

    UNIQUE READS: Uniquely mapped reads number | 5897884 Uniquely mapped reads % | 82.49% Average mapped length | 200.55 Number of splices: Total | 4359122 Number of …

  8. 转录组结题报告

    https://adamtongji.github.io/RNApipe/templates/mapping_summary.html

    1) Number of input reads：RNA-seq原始数据下机处理后，参考序列比对分析中输入序列数目统计； 2) Average input read length：序列平均长度统计； 3) Uniquely mapped reads number： …

  9. get uniquely mapped reads vs reads mapped at multiple …

    https://gist.github.com/sbamin/27acf13f2a28161efbf89a273559bca4

    2022年3月19日 · Here is a one-liner to get uniquely mapped reads, however this is quite slow and unstable. Read answer at stackexchange samtools view -@ 6 -q 1 -F 4 -F 256 -h mybam.bwa …

  10. Less multimapping reads, more uniquely mapped reads · Issue …

    https://github.com/alexdobin/STAR/issues/215

    2016年11月23日 · But I get more uniquely aligned reads with Tophat2: Reads: Input : 10206806 Mapped : 10058745 (98.5% of input) of these: 347302 ( 3.5%) have multiple alignments (2093 …

  11. Problems to Extract uniquely mapping reads from BWA …

    https://bioinformatics.stackexchange.com/questions/2404

    Every read can be mapped to multiple places if you allow enough mismatches. You heard "unique mapping" from time to time. Strictly speaking, however, this concept is either ill defined …

  12. Question: Are all output reads from STAR uniquely …

    https://github.com/alexdobin/STAR/issues/293

    2017年7月18日 · If you want unique mappers only, you would need --outFilterMultimapNmax 1 . In your example, I am not sure why filtered.bam contains more reads than …

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