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RNA-seq
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README.mkdn

README.mkdn 2.4 KB
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  1. RNA-seq data were analyzed using 5 different quantification strategies
    2. 

  2. and 2 different transcriptome annotations, for 10 total analyses.
    3. 

  3. 

  4. ## Data exploration and QC reports
    5. 

  5. 

  6. - [`hisat2_grch38_snp_tran_ensembl.85-exploration.html`](hisat2_grch38_snp_tran_ensembl.85-exploration.html)
    7. 

  7. - [`hisat2_grch38_snp_tran_knownGene-exploration.html`](hisat2_grch38_snp_tran_knownGene-exploration.html)
    8. 

  8. - [`kallisto_hg38.analysisSet_ensembl.85-exploration.html`](kallisto_hg38.analysisSet_ensembl.85-exploration.html)
    9. 

  9. - [`kallisto_hg38.analysisSet_knownGene-exploration.html`](kallisto_hg38.analysisSet_knownGene-exploration.html)
    10. 

  10. - [`salmon_hg38.analysisSet_ensembl.85-exploration.html`](salmon_hg38.analysisSet_ensembl.85-exploration.html)
    11. 

  11. - [`salmon_hg38.analysisSet_knownGene-exploration.html`](salmon_hg38.analysisSet_knownGene-exploration.html)
    12. 

  12. - [`shoal_hg38.analysisSet_ensembl.85-exploration.html`](shoal_hg38.analysisSet_ensembl.85-exploration.html)
    13. 

  13. - [`shoal_hg38.analysisSet_knownGene-exploration.html`](shoal_hg38.analysisSet_knownGene-exploration.html)
    14. 

  14. - [`star_hg38.analysisSet_ensembl.85-exploration.html`](star_hg38.analysisSet_ensembl.85-exploration.html)
    15. 

  15. - [`star_hg38.analysisSet_knownGene-exploration.html`](star_hg38.analysisSet_knownGene-exploration.html)
    16. 

  16. 

  17. ## Differential expression reports
    18. 

  18. 

  19. - [`hisat2_grch38_snp_tran_ensembl.85-diffexp.html`](hisat2_grch38_snp_tran_ensembl.85-diffexp.html)
    20. 

  20. - [`hisat2_grch38_snp_tran_knownGene-diffexp.html`](hisat2_grch38_snp_tran_knownGene-diffexp.html)
    21. 

  21. - [`kallisto_hg38.analysisSet_ensembl.85-diffexp.html`](kallisto_hg38.analysisSet_ensembl.85-diffexp.html)
    22. 

  22. - [`kallisto_hg38.analysisSet_knownGene-diffexp.html`](kallisto_hg38.analysisSet_knownGene-diffexp.html)
    23. 

  23. - [`salmon_hg38.analysisSet_ensembl.85-diffexp.html`](salmon_hg38.analysisSet_ensembl.85-diffexp.html)
    24. 

  24. - [`salmon_hg38.analysisSet_knownGene-diffexp.html`](salmon_hg38.analysisSet_knownGene-diffexp.html)
    25. 

  25. - [`shoal_hg38.analysisSet_ensembl.85-diffexp.html`](shoal_hg38.analysisSet_ensembl.85-diffexp.html)
    26. 

  26. - [`shoal_hg38.analysisSet_knownGene-diffexp.html`](shoal_hg38.analysisSet_knownGene-diffexp.html)
    27. 

  27. - [`star_hg38.analysisSet_ensembl.85-diffexp.html`](star_hg38.analysisSet_ensembl.85-diffexp.html)
    28. 

  28. - [`star_hg38.analysisSet_knownGene-diffexp.html`](star_hg38.analysisSet_knownGene-diffexp.html)
    29. 

  29. 

  30. ## Comparison between quantification strategies
    31. 

  31. 

  32. - [`rnaseq-compare.html`](rnaseq-compare.html)
    33.