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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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.htmlLast edited by GenoMax; 10-17-2013, 02:17 PM.
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Originally posted by GenoMax View PostSorted 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
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Originally posted by GenoMax View PostWhat genome are you working with?
Have you indexed your sorted BAM?Code:$samtools index sorted.bam
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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Originally posted by KnowNothing2 View PostI 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.
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Originally posted by GenoMax View PostYou 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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