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Old 10-17-2013, 02:08 PM   #1
KnowNothing2
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Default what's the difference between a bam and a sorted bam

I have both and don't know what to do with either (i.e. how to analyze). I was going to use NCBI genome workbench since it seemed to be the least convoluted and it works with windows.
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Old 10-17-2013, 02:15 PM   #2
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Sorted BAM has the data sorted by chromosomes/contigs/scaffolds whatever is in your reference genome. In order to efficiently display/access the data the BAM file has to be sorted.

For viewing aligned/sorted BAM files use integrated genome viewer (IGV) on windows. Unfortunately Broad's website appears to be down for maintenance till Monday but the URL you will want is: http://www.broadinstitute.org/igv/

You can try IGB in the mean time: http://bioviz.org/igb/index.html

Last edited by GenoMax; 10-17-2013 at 02:17 PM.
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Old 10-17-2013, 02:32 PM   #3
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Quote:
Originally Posted by GenoMax View Post
Sorted BAM has the data sorted by chromosomes/contigs/scaffolds whatever is in your reference genome. In order to efficiently display/access the data the BAM file has to be sorted.

For viewing aligned/sorted BAM files use integrated genome viewer (IGV) on windows. Unfortunately Broad's website appears to be down for maintenance till Monday but the URL you will want is: http://www.broadinstitute.org/igv/

You can try IGB in the mean time: http://bioviz.org/igb/index.html
Thanks for the info. Unfortunately, it's IGB is not allowing me to install the program and keeps saying error:could not create a virtual java machine.
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Old 10-17-2013, 02:37 PM   #4
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Scratch that, I was able to download the low memory version, even though my computer was 4Gb of ram... I am able to open my .sam file in IGB but neither of my .bam (bam and sorted bam) will open. It says "Failed to authenticate server" when I try to open file.
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Old 10-17-2013, 02:58 PM   #5
GenoMax
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What genome are you working with?

Have you indexed your sorted BAM?
Code:
$samtools index sorted.bam
Here is another option to try: http://bioinf.scri.ac.uk/tablet/

Last edited by GenoMax; 10-17-2013 at 03:03 PM.
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Old 10-17-2013, 03:10 PM   #6
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Quote:
Originally Posted by GenoMax View Post
What genome are you working with?

Have you indexed your sorted BAM?
Code:
$samtools index sorted.bam
Here is another option to try: http://bioinf.scri.ac.uk/tablet/
I used Bowtie 2 to align against MM10 (mouse genome).

I have not yet created an indexed BAM since the bowtie 2 manual didn't mention anything about that. But it looks like it's required, so I"ll do that tomorrow when I'm at my Linux computer.

It looks like my SAM file is aligning to IGB mRNA but I don't know what the genes are since they're given cryptic names.
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Old 10-17-2013, 03:58 PM   #7
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Quote:
Originally Posted by KnowNothing2 View Post
I used Bowtie 2 to align against MM10 (mouse genome).

It looks like my SAM file is aligning to IGB mRNA but I don't know what the genes are since they're given cryptic names.
You can download the mm10 GTF file here: ftp://ftp.ensembl.org/pub/current_gt...Cm38.73.gtf.gz IGB should be able to open that and give you gene annotations.
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Old 10-17-2013, 04:00 PM   #8
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Quote:
Originally Posted by GenoMax View Post
You can download the mm10 GTF file here: ftp://ftp.ensembl.org/pub/current_gt...Cm38.73.gtf.gz IGB should be able to open that and give you gene annotations.
Okay, I figured if I just downloaded an MM10 genome I'd be able to reference (right now I'm using Tablet). that said, I began downloading the mm10 genome from the Bowtie 2 website. Hopefully that does it.
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