Brief history
Bioinformatics expertise: Novice
Objective: Want to compile bam index files to view aligned reads in IGV.
Starting materials: downloaded Perl, latest samtools, and have ~30 bam files ready and eager to visualize.
OS: Windows 7 64-bit
I am not a computer scientist. I have no intention of learning all there is to know about command line bioinformatics. Someone please give me a point-by-point explanation of how I go about generating bam index files all the way up from opening the correct terminal to executing the command. Every manual I have found about samtools assumes that I have some working knowledge of command line....I have none. Don't know how to proceed from opening a command terminal to building in samtools or assigning directories or anything.
Keep it simple--assume I am 5.
Bioinformatics expertise: Novice
Objective: Want to compile bam index files to view aligned reads in IGV.
Starting materials: downloaded Perl, latest samtools, and have ~30 bam files ready and eager to visualize.
OS: Windows 7 64-bit
I am not a computer scientist. I have no intention of learning all there is to know about command line bioinformatics. Someone please give me a point-by-point explanation of how I go about generating bam index files all the way up from opening the correct terminal to executing the command. Every manual I have found about samtools assumes that I have some working knowledge of command line....I have none. Don't know how to proceed from opening a command terminal to building in samtools or assigning directories or anything.
Keep it simple--assume I am 5.
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