| Bam directory: | /crex/proj/snic2019-30-56/lilit/fivepseq_projects/microbiome/atlas_bam/ecol/*.bam |
| Bam files: | ecol_ctr_r1_s_r_v1 ecol_ctr_r2_s_r_v1 ecol_ctr_r3_s_r_v1 |
| Genome file: | /crex/proj/snic2019-30-56/lilit/fivepseq_projects/microbiome/genome/single/ecol-GCF_000005845.2/fa/GCF_000005845.2_ASM584v2_genomic.fna |
| Annotation file: | /crex/proj/snic2019-30-56/lilit/fivepseq_projects/microbiome/genome/single/ecol-GCF_000005845.2/gff/GCF_000005845.2_ASM584v2_genomic.gff |
| Gene set file: | None |
| Gene filter file: | None |
| Output directory: | /crex/proj/snic2019-30-56/lilit/fivepseq_projects/microbiome/atlas_fivepseq/ecol/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) |
|---|---|
| ecol_ctr_r1_s_r_v1 | 0.92899 |
| ecol_ctr_r2_s_r_v1 | 0.93352 |
| ecol_ctr_r3_s_r_v1 | 0.97952 |
| Main report | main/ecol_main.html |
| Combined samples | main/ecol_combined.html |
| Amino acid line-charts | supplement/ecol_amino_acid_linecharts.html |
| Codon line-charts: | supplement/ecol_codon_linecharts.html |
| Codon heatmaps: | supplement/ecol_codon_heatmaps.html |
| Dipeptide linecharts: | supplement/ecol_dipeptide_linecharts.html |
| Tripeptide linecharts: | supplement/ecol_tripeptide_linecharts.html |
| Dicodon linecharts: | supplement/ecol_dicodon_linecharts.html |
| Tricodon linecharts: | supplement/ecol_tricodon_linecharts.html |
| Differential heatmaps: | comparison/ecol_differential_heatmaps.html |
| Compare samples in each gene-set | None |
| Compare gene-sets in each sample | None |