Bam directory: | /crex/proj/snic2019-30-56/lilit/fivepseq_projects/microbiome/atlas_bam/ptim/*.bam |
Bam files: | ptim_ctr_r1_s_o_v15 ptim_ctr_r2_s_o_v15 |
Genome file: | /crex/proj/snic2019-30-56/lilit/fivepseq_projects/microbiome/genome/single/ptim-GCF_000430565.1/fa/GCF_000430565.1_ASM43056v1_genomic.fna |
Annotation file: | /crex/proj/snic2019-30-56/lilit/fivepseq_projects/microbiome/genome/single/ptim-GCF_000430565.1/gff/GCF_000430565.1_ASM43056v1_genomic.gff |
Gene set file: | None |
Gene filter file: | None |
Output directory: | /crex/proj/snic2019-30-56/lilit/fivepseq_projects/microbiome/atlas_fivepseq/ptim/fivepseq_plots |
Conflict mode: | add |
Span size: | 100 |
Transcript type: | protein_coding |
Outlier detection p value [--op]: | 0 |
Down-sampling constant [--ds] | None |
Masking transcript boundaries for codon counts [--no-mask --mask_codon_size]: | by 20 positions |
Dipeptide relative counts sorted at A-site relative position [--dipeptide_pos]: | -11 |
Tripeptide relative counts sorted at A-site relative position [--tripeptide_pos]: | -8 |
Sample | Library size (M) |
---|---|
ptim_ctr_r1_s_o_v15 | 1.26581 |
ptim_ctr_r2_s_o_v15 | 1.61036 |
Main report | main/ptim_main.html |
Combined samples | main/ptim_combined.html |
Amino acid line-charts | supplement/ptim_amino_acid_linecharts.html |
Codon line-charts: | supplement/ptim_codon_linecharts.html |
Codon heatmaps: | supplement/ptim_codon_heatmaps.html |
Dipeptide linecharts: | supplement/ptim_dipeptide_linecharts.html |
Tripeptide linecharts: | supplement/ptim_tripeptide_linecharts.html |
Dicodon linecharts: | supplement/ptim_dicodon_linecharts.html |
Tricodon linecharts: | supplement/ptim_tricodon_linecharts.html |
Differential heatmaps: | comparison/ptim_differential_heatmaps.html |
Compare samples in each gene-set | None |
Compare gene-sets in each sample | None |