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SNPs

NEEDS

  • vcf file
  • gtf file (Ensembl)
  • csv files with go annotations (Biomart ENsembl)

Using the SNP pipeline:

  • Usage:

tmp_scripts_using_pyGen.py snps -s file.vcf -a file.gtf - g biomart.csv

  • Example:

~/bin/pyGen/tmp_scripts_using_pyGen.py snps -s round2_HQ_SNP.vcf -a~/bin/pyGen/demo_data/Zfinch/Taeniopygia_guttata.taeGut3.2.4.77.gtf -g ~/bin/pyGen/demo_data/Zfinch/zfinch_go_annot.csv

Differential expression

Make DE test using DE_with_edgeR.R

Example:

DE_with_edgeR.R all_counts_junco junco_sample_grps.tab 4 exact myout1 2 transcripts_ensembl.tab