Ploytbag

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MasonLab

TBAG

TBAG_Tutorial

polytbag

The polytbag annotation with provide predicted information including putative polyA tail site, gene name, transcript ID and the exon number.

$ cd ~/Desktop/TBAG/TBAG/polytbag
$ ./polytbag ../../preprocessing/polya.sam ../../preprocessing/polyt.sam ../../genome/AceView/ polytbagOutput

The output format is following. If one putative polyA tail site can be assigned to multiple transcripts, the "transcript_ID#exon_number" will be given and different transcripts will be seperated by ";".

chr     putative_pola_site      polyA_tail_base_num     read_counts     strand  gene    transcript#exon_num;
chr10   104230507       6,      1       -       ACTR1A  ACTR1A.bApr07#11;ACTR1A.cApr07#11;ACTR1A.dApr07#10;ACTR1A.hApr07#4;ACTR1A.jApr07#3;
chr10   32364487        6,      1       -       KIF5B   KIF5B.aApr07#10;
chr11   64657574        6,      1       -       SYVN1   SYVN1.aApr07#2;SYVN1.bApr07#2;SYVN1.cApr07#2;SYVN1.dApr07#2;SYVN1.eApr07#2;SYVN1.iApr07#1;SYVN1.jApr07#1;