Question for people working with SAM files in genome alignments

Anonymous Monk has asked for the wisdom of the Perl Monks concerning the following question:

Replies are listed 'Best First'.
Re: Question for people working with SAM files in genome alignments by marto (Cardinal) on Dec 21, 2017 at 16:02 UTC
Like Laurent_R I don't understand the question, if you can't explain the problem in a way that it can be relatively easily understood perhaps talk to bioperl people on IRC or their mailing list? http://bioperl.org/Support.html. Also How do I post a question effectively?/I know what I mean. Why don't you?.	[reply]
Re: Question for people working with SAM files in genome alignments by Laurent_R (Canon) on Dec 21, 2017 at 15:39 UTC
Hi, I am not a geneticist and I don't understand your question. As I suppose that many monks here are in a similar situation, it might be worth for you to try to explain what you're trying to do in words that will be understood by people having a limited or no biological background.	[reply]
Re^2: Question for people working with SAM files in genome alignments by BillKSmith (Monsignor) on Dec 22, 2017 at 18:08 UTC
This may be the rare exception to our rules for posting an effective question. The OP appears not to be seeking help with perl progamming, but rather, seeking a tool (possibly written in perl) to solve his genetics problem. I hope that someone will be able to help him. Bill	[reply]
Re: Question for people working with SAM files in genome alignments by karlgoethebier (Abbot) on Dec 22, 2017 at 20:51 UTC
I have no clue. But you might take a look at htslib.org and SAMTools. Don't know if this helps. Regards, Karl PS.: For the other uninitiated: SAM ŤThe Crux of the Biscuit is the Apostropheť `perl -MCrypt::CBC -E 'say Crypt::CBC->new(-key=>'kgb',-cipher=>"Blowfish")->decrypt_hex($ENV{KARL});'`Help	[reply] [d/l]
Re: Question for people working with SAM files in genome alignments by ablanke (Monsignor) on Dec 23, 2017 at 11:37 UTC
Hi, SuperSearch revealed this three nodes: cigar string string manipulation with Regex Matching strings from three files (three hashes) You could also search on CPAN Or go through the index of Bio modules on CPAN https://www.cpan.org/modules/by-module/Bio/ hope it helps	[reply]