generateCracSummary.pl - Generate Crac's summary from SAM file
generateCracSummary.pl file.sam > file.summary
Create the crac summary report from a sam, sam.gz or bam file. You will get something like :
---------------------------------- Some STATISTICS
---------------------------------- Total number of reads analyzed: 68736346
Single: 57784025 (84.0662%) Multiple: 4617008 (6.71698%) None: 534816 (0.778069%) Duplication: 23813841 (34.6452%)
Warning: the sum of the four previous categories may not be equal to 100%. This is normal: reads are considered by chunks. In a given read, a chunk may appear multiple times, while another just appears once.
---------------------------------- Explainable: 66335353 (96.507%)
Repetition: 1927356 (2.80398%) Normal: 18503376 (26.9193%) Almost-Normal: 11796568 (17.1621%) Sequence-Errors: 10316781 (15.0092%) SNV: 2222562 (3.23346%) Short-Indel: 71294 (0.103721%) Splice: 3047373 (4.43342%) Weak-Splice: 1994 (0.00290094%) Chimera: 648997 (0.944183%) Paired-end Chimera: 7369210 (10.721%) Bio-Undetermined: 15408195 (22.4164%) Undetermined: 1965574 (2.85958%)
To install CracTools, copy and paste the appropriate command in to your terminal.
cpanm
cpanm CracTools
CPAN shell
perl -MCPAN -e shell install CracTools
For more information on module installation, please visit the detailed CPAN module installation guide.