UC Davis TAMA Tutorial 6 - GenomeRIK/workshop_tutorials GitHub Wiki

Using TAMA Degradation Signature

change directory 

  cd 3_tc_flnc_nolde_c

make bash script 

  run_tama_collapse.sh

fill bash script 

  spath='/share/workshop/isoseq_workshop/rkuo/tama/'
  pscript='tama_collapse.py'
  capflag='capped'
  fpath='/share/workshop/isoseq_workshop/rkuo/2_map/'
  sam='mm2_alz_flnc_hg38_sort.bam'
  fasta='/share/workshop/isoseq_workshop/rkuo/1_data/hg38.fa'
  prefix=`echo ${sam} | sed 's/\.bam//' | awk '{print "tc_c_flnc_nolde_"$1}' `
  python ${spath}${pscript} -s ${fpath}${sam} -f ${fasta} -p ${prefix} -d merge_dup -x ${capflag} -a 100 -z 100 -sj sj_priority -sjt 10 -log log_off -b BAM

run bash script 

  sh run_tama_collapse.sh

change directory 

  cd 5_degsig

make bash script 

  run_degsig.sh

fill bash script 

  spath='/share/workshop/isoseq_workshop/rkuo/tama/tama_go/file_stats/'
  pscript='tama_degradation_signature.py'
  capped='/share/workshop/isoseq_workshop/rkuo/3_collapse/3_tc_flnc_nolde_c/tc_c_flnc_nolde_mm2_alz_flnc_hg38_sort_trans_read.bed'
  nocap='/share/workshop/isoseq_workshop/rkuo/3_collapse/2_tc_flnc_nolde_nc/tc_nc_flnc_nolde_mm2_alz_flnc_hg38_sort_trans_read.bed'
  outfile='degsig_tc_flnc_nolde.txt'
  python ${spath}${pscript}  -c ${capped} -nc ${nocap} -o ${outfile}

run bash script 

  sh run_degsig.sh
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