[BioC] deqseq_count and BWA-based SAM files

[Steve Lianoglou]

I'd rather use `samtools sort ...`

You probably want to (1) convert your sam to bam, (2) then sort, (3)
then index, (4) then use.

>From the command line:

## convert to bam
samtools view -bS your.sam > your-tmp.bam

## sort bam
samtools sort your-tmp.bam your

## index bam
samtools index your.bam

Now you can junk your sam file and save mucho HD space to boot.

-steve

On Tue, Dec 13, 2011 at 10:41 AM, wang peter <wng.peter at gmail.com> wrote:
> you can sort them by linux command
>
> sort -T . -S 2G -k 1,1 -k 3,3 $target_fa.psl.sam > $target_fa.psl.nameSorted.sam
> --
> shan gao
> Room 231(Dr.Fei lab)
> Boyce Thompson Institute
> Cornell University
> Tower Road, Ithaca, NY 14853-1801
> Office phone: 1-607-254-1267(day)
> Official email:sg839 at cornell.edu
> Facebook:http://www.facebook.com/profile.php?id=100001986532253
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact