UC Davis 2021 Exercise 3 - GenomeRIK/workshop_tutorials GitHub Wiki

Using TAMA Merge to compare Iso-Seq annotation with Gencode/Ensembl and RefSeq/NCBI

Look at the input file list file for TAMA Merge 

  filelist_trio.txt

The file should look like this: 

  tc_nc_lde220_mm2_alz_flnc_hg38_sort_chrom_cleanup.bed   no_cap  2,2,2   isoseq
  gencode.v33_chrom_cleanup.bed   capped  1,1,1   gencode
  refseq_only_GRCh38_latest_genomic_chrom_convert.bed     capped  1,1,1   refseq

Note that fields are tab separated!

Look at bash script 

  run_tama_merge_trio.sh

Bash script should look like: 

  filelist='filelist_trio.txt'
  prefix='tm_trio_100'
  fivethresh='100'
  threethresh='100'
  source='gencode,refseq'
  spath='/home/genomerik/tama/'
  pscript='tama_merge.py'
  python ${spath}${pscript} -f ${filelist} -p ${prefix} -a ${fivethresh} -z ${threethresh} -d merge_dup -s ${source}

run bash script 

  sh run_tama_merge_trio.sh

Check out the summary run bash script 

 sh run_summary.bed tm_trio_100.bed

Let's take a look at the file in IGV!

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