[Bioc-sig-seq] Rsamtools scanBam output to Bam

[burak kutlu]

HI Sean,
I am using the output of a RNAseq pipeline that includes some reads that I do not want to use (I have no control over the stringency of alignments). Indeed, it is straight-forward to load big BAM files to IGV
Thanks
-burak



----- Original Message ----
From: Sean Davis <seandavi at gmail.com>
To: burak kutlu <burak_kutlu at yahoo.com>
Cc: bioc-sig-sequencing at r-project.org; pshannon at systemsbiology.org
Sent: Mon, April 12, 2010 11:13:45 AM
Subject: Re: [Bioc-sig-seq] Rsamtools scanBam output to Bam

On Mon, Apr 12, 2010 at 12:35 PM, burak kutlu <burak_kutlu at yahoo.com> wrote:
> Hi
> Is there a way to create a SAM file from the output of scanBam from Rsamtools?
> The reason we would like to do is use IGV to visualize a subset of regions in a large Bam file using load2newIGV function from SRAdb.
> For this, we will need to put the list structure back to SAM format.
> Please let me know if this is enough to give you an idea what we are trying to achieve.
> Thanks in advance

Hi, Burak.

You shouldn't need to subset the BAM file into regions.  IGV will load
HUGE BAM (we have loaded 200x coverage human genome) files without a
problem since it reads only the part of the file necessary and does
not store large files in memory.  And you will definitely want to use
BAM and not SAM for IGV.

Sean