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
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
Comment