fivepseqfivepseq
         

ptim

Input and run configurations

Main input:

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

Auxiliary files

Gene set file: None
Gene filter file: None

Other options

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
   

Summary statistics

SampleLibrary size (M)
ptim_ctr_r1_s_o_v151.26581
ptim_ctr_r2_s_o_v151.61036
   

Report files

Main

Main report main/ptim_main.html
Combined samples main/ptim_combined.html

Supplement

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

Comparisons

Differential heatmaps: comparison/ptim_differential_heatmaps.html

Gene sets

Compare samples in each gene-set None
Compare gene-sets in each sample None