Star quantmode. --quantMode GeneCounts options?

Discussion in 'add' started by Maushakar , Wednesday, February 23, 2022 11:27:45 AM.

  1. Nikolabar

    Nikolabar

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    Skip to main content. Comparison of sets of differentially expressed transcripts, and their overlaps, computed using each method. To test the hypothesis that disallowing indels in the alignments will adversely affect quantification accuracy when simulating from a reference transcriptome containing realistic variants compared to the reference, we performed the following experiment. In response to improvements in RNA-seq quality and read lengths, as well as significant improvements in the available quantification methods, it has also become increasingly common to perform quantification and differential testing at the transcript level. Add the following code to your website. Thanks alexdobin. We used Salmon v1.
    read counts - Star quantmode. BANDITS: Bayesian ANalysis of DIfferenTial Splicing
     
  2. Moshura

    Moshura

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    With --quantMode GeneCounts option STAR will count number reads per gene while mapping. A read is counted if it overlaps (1nt or more) one.You can try to run it on the unsorted file without this option, and hopefully, you will reproduce the correct counts.
    Star quantmode. Alignment and mapping methodology influence transcript abundance estimation
     
  3. Gardakus

    Gardakus

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    cumperi.online › skrabanek › lab › angsd › lecture_notes.Since I have different values for columns 3 and 4, does that automatically mean that I have strand-specific data?
     
  4. Akinobei

    Akinobei

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    Hi, The STAR is such a good tool to do the alignment, and I really like it. Recently, I used the --quantMode GeneCounts to get the count.The transcript-level counts were summed to the gene level using tximport [ 37 ], and differential expression analysis was performed using DESeq2 [ 38 ].
     
  5. Megal

    Megal

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    forum? STAR alignment · Alignment is run with 6 threads --runThreadN 6 · The --quantMode TranscriptomeSAM option generates alignments translated into transcript.Moreover, the SA approach can take as input a set of decoy sequences, enabling it to avoid some of the spurious transcriptome mappings reported by Bowtie2, when, in reality, the read aligns better to an unannotated genomic locus than to the annotated transcriptome.
     
  6. Telrajas

    Telrajas

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    Sequence reads were aligned to the human genome hg19 using STAR. STAR quantMode was used to obtain raw read counts. Assembly: hgA read is counted if it overlaps 1nt or more one and only one gene.Forum Star quantmode
     
  7. Goltiramar

    Goltiramar

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    Trimmed reads were aligned mm10 genome assembly, indexed to GENCODE (vM16) GFF3 annotation via STAR aligner with flag '--quantMode.Subsequently, we quantified all samples using each of the remaining pipelines.
     
  8. Gogar

    Gogar

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    The cumperi.online output files of STAR (from option –quantMode GeneCounts) contain 4 columns that correspond to different counts per gene calculated.SA takes steps toward addressing the shortcomings of existing alignment-based approaches without making large compromises on speed.Forum Star quantmode
     
  9. Mooguran

    Mooguran

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    We've switched over to using STAR for all our RNA-Seq alignments and I'm happy to see the addition of generating gene counts with --quantMode GeneCounts.For example, spliced alignment of sequencing reads to the genome can be done in the absence of an annotation of known isoforms and can be used to help identify novel exons, isoforms, or transcribed regions of the genome, while unspliced alignment to a pre-specified set of transcripts does not admit this type of analysis.
     
  10. Kerisar

    Kerisar

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    Data processing, A human genome reference index was built by STAR b file with reads per gene counts from STAR -quantMode GeneCounts.Lih-Ling Lin, and Shanrong Zhao.Forum Star quantmode
     
  11. Gojora

    Gojora

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    Hello Everyone, I have problems with STAR aligner. I want to use the quantMode option in order to cumperi.online file that I will use for later.We also demonstrate that, even among alignment-based approaches, non-trivial differences arise between quantifications based upon mapping to the transcriptome using Bowtie2 [ 12 ] and quantifications based upon mapping to the genome and subsequently projecting these alignments into transcriptomic coordinates using STAR [ 19 ].
     
  12. Nekasa

    Nekasa

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    STAR quantMode (GeneCounts) essentially provides the same output as HTSeq-Count would, ie. number of reads that cover a given gene.Polyester: simulating RNA-seq datasets with differential transcript expression.
     
  13. Mikanris

    Mikanris

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    a14, inserting annotations on the fly: STAR --quantMode TranscriptomeSAM --alignIntronMin 20 --alignIntronMax --outFilterMismatchNmax.See Schurch et al, ; arXivForum Star quantmode
     
  14. Zolobei

    Zolobei

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    With --quantMode GeneCounts option STAR will count number reads per gene while mapping. A read is counted if it overlaps (1nt or more) one and only one gene.Is that the reason for differences in results?
     
  15. Zulujinn

    Zulujinn

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    STAR—Alignment with STAR to the target genome (aided with the GTF output by STAR via the –quantMode TranscriptomeSAM flag (as would be.Performance of each method on real bulk and single-cell datasets.
     
  16. Vusida

    Vusida

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    With --quantMode TranscriptomeSAM option, STAR will output alignments translated into transcript coordinates in the cumperi.online file (in.The design of this study will highlight how misquantifications, possibly arising from incorrect alignments, can affect DGE analysis.
    Star quantmode.
     
  17. Mazuran

    Mazuran

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    We counted reads mapping to exons using the "--quantMode GeneCounts" option (version STAR_a_modified) (Dobin et al., ; Dobin & Gingeras, ).At the same time, we proposed and benchmarked a new hybrid alignment method, SA, which provides an efficient alternative to lightweight mapping that produces results much closer to what is obtained by performing traditional alignment.
    Star quantmode.
     
  18. Tygoshura

    Tygoshura

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    RNA-seq reads were aligned to UCSC hg19 using STAR version a Only uniquely mapping reads with at Gene count tables were output from STAR quantMode.Then, from these reduced statistics, abundance estimation is performed.
     
  19. Arashigrel

    Arashigrel

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    forum? NOTE: when using salmon, use the option --dumpEq to obtain the equivalence classes, when using STAR, use the option --quantMode TranscriptomeSAM to obtain.Reads derived from unannotated genomic regions that bear resemblance to annotated transcripts, or which only partially overlap the annotated features, can then be spuriously aligned to the annotated features, leading to inaccurate quantification of their abundances.Forum Star quantmode
     
  20. Aragor

    Aragor

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    The use of the –quantMode GeneCounts option in STAR produces and identical output as the one from htseq-count. As the accuracy of quantification relies.Therefore, quantification is a crucial step for accurate differential gene expression DGE estimation and other downstream analyses.
     
  21. Nekazahn

    Nekazahn

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    To explore some of the transcripts with large differences in quantification across methods, we performed differential transcript expression analysis across methods on the samples, using limma-trend [ 33 ].
    Star quantmode.
     
  22. Dilabar

    Dilabar

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    We posit that this is because, though great advancements have been made in improving the realism of simulated RNA-seq data, these simulations still fail to capture some of the complexities of experimental data.
     
  23. Malagore

    Malagore

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    Good explanation.
     
  24. Mezicage

    Mezicage

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    Bioinformatics Stack Exchange works best with JavaScript enabled.
    Star quantmode.
     
  25. Mazur

    Mazur

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    Cell Stem Cell.
    Star quantmode.
     
  26. Meztikora

    Meztikora

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    Errors in quantification can affect differential expression analysis not just at the gene level, but at the transcript level as well.
     
  27. Daimuro

    Daimuro

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    Select the output according to the strandedness of your data.
     

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