[BioC] deqseq_count and BWA-based SAM files

[Wyatt McMahon]

Thanks to everyone who has replied to this.  I really appreciate it!

Unfortunately, none of these has worked.  I've used both Shan's script as well as samtools and am still having the same problem.  Despite everything being very nicely sorted, I still getting the same error message.

I'm not sure what to do.  I may write the developer of the dexseq_count script. . . .

Thanks so much,

Wyatt

----- Original Message -----
From: "Steve Lianoglou" <mailinglist.honeypot at gmail.com>
To: "wang peter" <wng.peter at gmail.com>
Cc: "Wyatt McMahon [guest]" <guest at bioconductor.org>, bioconductor at r-project.org, wmcmahon at vbi.vt.edu
Sent: Tuesday, December 13, 2011 4:02:01 PM
Subject: Re: [BioC] deqseq_count and BWA-based SAM files

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
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-- 
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