UC Davis TAMA Tutorial 3 - GenomeRIK/workshop_tutorials GitHub Wiki

Using TAMA Merge to compare cluster annotation vs flnc annotation

change directory

  cd 4_merge

Make folders

  1_merge_tc_cluster_cupcake
  2_merge_flnc_cluster
  3_merge_flnc_gencode

change directory

  cd 2_merge_flnc_cluster

copy TAMA Collapse annotation from cluster here

  cp ../../3_collapse/1_tc_cluster_nolde_nc/tc_nc_nolde_cluster_alz.aligned.bed .

copy TAMA Collapse annotation from FLNC here

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

make file

  filelist.txt

fill file

use tab separation!

  tc_nc_nolde_cluster_alz.aligned.bed     no_cap  1,1,1   cluster
  tc_nc_flnc_nolde_mm2_alz_flnc_hg38_sort.bed     no_cap  1,1,1   flnc

make bash script

  run_tama_merge.sh

fill bash script

  filelist='filelist.txt'
  prefix='tm_flnc_cluster_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

make bash script

  run_summary_merge.sh

fill bash script

  echo ""
  echo "transcript level"
  echo ""
  transfile=`ls| grep "trans_report.txt"`
  cat ${transfile} | awk '{print $3}'| grep -v "sources" | sort | uniq -c
  echo ""
  echo "gene level"
  echo ""
  genefile=`ls| grep "gene_report.txt"`
  cat ${genefile} | awk '{print $4}' |grep -v "sources" | sort | uniq -c

run bash script

 sh run_summary_merge.sh