|
From: Duhaime J. <Joh...@ir...> - 2010-06-15 13:14:38
|
Hello I just installed samTools on Solaris 10 (SunOS 5.10 Generic_127128-11 i86pc i386 i86pc) with samtools-0.1.7a.tar.bz2<http://sourceforge.net/projects/samtools/files/samtools/0.1.7/samtools-0.1.7a.tar.bz2/download> Installation went OK (I could not installed in 64 bits but this is another problem). But I cannot make the program work as shown below. The SAM file input is from "bowtie -S". Here are the many tries I have done: -chmod 777 on my input file -run the program as ROOT -looking on the web, someone suggests to run the program from the directory where it is installed, which I did. -run MACS with -aligner SAM which was a success (so my file is recognized as a Sam file) -as said I went through the web to look for that problem, but most of the time the solution was not there. I would appreciate very much if you could help me. Thank you in advance. # ./samtools view Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]] Options: -b output BAM -h print header for the SAM output -H print header only (no alignments) -S input is SAM -u uncompressed BAM output (force -b) -x output FLAG in HEX (samtools-C specific) -X output FLAG in string (samtools-C specific) -t FILE list of reference names and lengths (force -S) [null] -T FILE reference sequence file (force -S) [null] -o FILE output file name [stdout] -f INT required flag, 0 for unset [0] -F INT filtering flag, 0 for unset [0] -q INT minimum mapping quality [0] -l STR only output reads in library STR [null] -r STR only output reads in read group STR [null] -? longer help # ./samtools view -S s_3.sam [main_samview] fail to open file for reading. Johanne Duhaime IRCM du...@ir... |