UC Davis TAMA Tutorial 4 - GenomeRIK/workshop_tutorials GitHub Wiki

Using TAMA Merge to compare flnc annotation to Gencode annotation

change directory 

  cd 1_data

make bash script 

  run_gencode_bed.sh

fill bash script 

  spath='/share/workshop/isoseq_workshop/rkuo/tama/tama_go/format_converter/'
  pscript='tama_format_gtf_to_bed12_ensembl.py'
  gff='gencode.v33.gtf'
  bed='gencode.v33.bed'
  python ${spath}${pscript} ${gff} ${bed}

run bash script 

  sh run_gencode_bed.sh

change directory 

  cd ../4_merge/3_merge_flnc_gencode

copy gencode bed file here 

  cp ../../1_data/gencode.v33.bed .

copy FLNC bed file here 

  cp ../../3_collapse/2_tc_flnc_nolde_nc/tc_nc_flnc_nolde_mm2_alz_flnc_hg38_sort.bed .

make filelist file 

  filelist.txt

fill filelist file

note tab separated!! 

  tc_nc_flnc_nolde_mm2_alz_flnc_hg38_sort.bed     no_cap  2,2,2   flnc
  gencode.v33.bed capped  1,1,1   gencode

make bash script 

  run_tama_merge.sh

fill bash script 

  filelist='filelist.txt'
  prefix='tm_flnc_gencode_100'
  fivethresh='100'
  threethresh='100'
  spath='/share/workshop/isoseq_workshop/rkuo/tama/'
  pscript='tama_merge.py'
  python ${spath}${pscript} -f ${filelist} -p ${prefix} -a ${fivethresh} -z ${threethresh} -d merge_dup

run bash script 

  sh run_tama_merge.sh

copy bash script 

  cp ../2_merge_flnc_cluster/run_summary_merge.sh .

run bash script 

  sh run_summary_merge.sh

download files

tm_flnc_gencode_100.bed

view in IGV 

  https://igv.org/app/

go to region 

  chr10:13,093,008-13,159,969
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