UC Davis TAMA Tutorial 7 - GenomeRIK/workshop_tutorials GitHub Wiki

Using TAMA read support and filtering

change directory 

  cd /3_collapse/2_tc_flnc_nolde_nc

make filelist file 

  filelist_read_support.txt

fill filelist file

note needs to be tab separated 

  1       tc_nc_flnc_nolde_mm2_alz_flnc_hg38_sort_trans_read.bed  trans_read

make bash script 

  run_read_support.sh

fill bash script 

  spath='/share/workshop/isoseq_workshop/rkuo/tama/tama_go/read_support/'
  pscript='tama_read_support_levels.py'
  filelist='filelist_read_support.txt'
  prefix='rs_tc_nc_flnc_nolde_mm2_alz_flnc_hg38'
  merge='no_merge'
  python ${spath}${pscript} -f ${filelist} -o ${prefix} -m ${merge}

run bash script 

  sh run_read_support.sh

make bash script 

  run_filter_singletons.sh

fill bash script 

  spath='/share/workshop/isoseq_workshop/rkuo/tama/tama_go/filter_transcript_models/'
  pscript='tama_remove_single_read_models_levels.py'
  bed='tc_nc_flnc_nolde_mm2_alz_flnc_hg38_sort.bed'
  readsupport='rs_tc_nc_flnc_nolde_mm2_alz_flnc_hg38_read_support.txt'
  prefix='fsm_tc_nc_flnc_nolde_mm2_alz_flnc_hg38'
  level='transcript'
  multi='keep_multi'
  numsources='1'
  python ${spath}${pscript} -b ${bed}  -r ${readsupport} -o ${prefix} -l ${level} -k ${multi} -s ${numsources}

run bash script 

  sh run_filter_singletons.sh
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