Supplementary Text from Concurrent loss of ciliary genes <i>WDR93</i> and <i>CFAP46</i> in phylogenetically distant birds

Contains all the Supplementary Text Sections S1 to S

Supplementary Tables from Concurrent loss of ciliary genes <i>WDR93</i> and <i>CFAP46</i> in phylogenetically distant birds

Contains all the Supplementary tables S1 to S1

Supplementary_File_S1 from Concurrent loss of ciliary genes <i>WDR93</i> and <i>CFAP46</i> in phylogenetically distant birds

Contains the pairwise alignment of Duck and Chicken genomes at the CFAP46 regio

Supplementary Figures from Concurrent loss of ciliary genes <i>WDR93</i> and <i>CFAP46</i> in phylogenetically distant birds

Contains all the Supplementary Figures S1 to S4

Differential expression analysis - edgeR

Differential expression analysis across the 2x10 libraries is performed using the Bioconductor packages edge

Simulate raw sequencing data - Step 2

The 2b_gnrCounts.R script generates per gene and per library expression levels for 2x10 libraries with differential expression among them. These read count files are used along with the fastq files simulated in previous step by 2c_drawreads.pl to create 2x10 libraries with differential expression among them

Compare mapping assemblies - Mapping 1

The quality of the mapping assemblies obtained after the consensus step is be evaluated

ZebraFinchData

Zebra finch CDS downloaded from Biomart (Ensembl Version 61) with 100 bp 5' UTR and 400 bp 3' UTR per gene

De novo assembly

In the next step, De novo assemblies need to be performed as per the computational infrastructure available. We provide an example commandline used by us

Metadata by individual

Metadata for each crow sampled in this study: including population of origin, GPS coordinates, dates of feather plucking, dates of sampling, times of day of sampling, weight at sampling, approximate age at sampling, and number of days of feather regrowth until sampling