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Old 02-04-2017, 11:01 AM   #1
Bean
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Location: Germany

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Default Indexing a Bam file with Samtools

Hi all,
after a break of 6 years (see my last post), I'm finally working with IGV again. This time, I'm not working with pre-indexed files, but have to check reference data for which only bam files are available, I have to index them myself. Only I just can't get the hang of it - everyone recommends Samtools, which I have downloaded, but I haven't the slightest idea how to actually run it under Windows (it seems to be ported from Linux, which I have never worked with in my life). Can anybody point me toward a dummy-proof tutorial on how to actually perform such indexing on Windows? I have been googling it for the better part of the day, and everything I have found up to now requires a certain kind of familiarity with the subject... As I am more or less on my own now (don't work in a lab any more, but need to finish a project), I don't have anyone I can ask.

It doesn't have to be Samtools - if there is any other Windows-friendly software out there with which I can index a bam file, that's fine with me...

I downloaded bam files from the European Nucleotide Archive - I don't know if any of the other formats would be easier for my purposes?

Thanks anyone who can help me out here (and I apologise about asking such a nooby question
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Old 02-04-2017, 11:18 AM   #2
Brian Bushnell
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I highly recommend you get access to Linux, or your bioinformatics capabilities will be somewhat crippled. This could mean dual booting, getting an account on a compute cluster, running a virtual machine (you can run a free virtual machine in Windows and install a free Linux distro in that virtual machine) doesn't really matter too much.

That said, try Picard:

https://broadinstitute.github.io/pic...-overview.html
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Old 02-04-2017, 11:41 AM   #3
Bean
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Thanks very much for the quick reply! Actually, I don't really do much in bioinformatics (hence the silly question), and I probably won't actually need it after this... I'll look into that link, thanks very much!
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Old 02-04-2017, 01:20 PM   #4
jdk787
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Have you tried using Galaxy?
https://usegalaxy.org/
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Old 02-04-2017, 01:46 PM   #5
Bean
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Just discovered the direct link via ENA to Galaxy, that's just it, thanks very much!
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