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gloriali / HirstLab

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WGS bam index #19

Open gloriali opened 8 years ago

gloriali commented 8 years ago

@SamMcConnell

I need index files to work with WGS bam files. I tried to generate them but seems I can't write to your folder. Could you run the following commands for me? Thanks! 

cd /projects/epigenomics/users/smcconnell/glioma/WGS/bam/
for file in *.bam; do
    echo $file
    /gsc/software/linux-x86_64-centos5/samtools-0.1.18/bin/samtools index $file
done
SamMcConnell commented 8 years ago

Sure thing, I'm running it now.

gloriali commented 8 years ago

@SamMcConnell

I saw you added A54762 for CEMT_47 to /projects/epigenomics2/users/lli/glioma/WGS/. But that one is WGBS library, not WGS.

SamMcConnell commented 8 years ago

@gloriali Oh, sorry I misread that. I'll go get the WGS one

SamMcConnell commented 8 years ago

@gloriali

I made a symlink to the merge folder. I don't have permission to use ls and look for the name of the merge file though and only the name of the directory is on Odin

gloriali commented 8 years ago

@SamMcConnell

Link it to /projects/edcc_prj2/upstream_data/P00015_8_lanes_dupsFlagged.bam. You can usually find this kind of information in CEMT project folder /projects/edcc_new/reference_epigenomes/.

SamMcConnell commented 8 years ago

@gloriali Thanks! It went through all of them except for CEMT_47. I didn't have permission for that one and the command halted. The rest are all indexed though.

gloriali commented 8 years ago

@SamMcConnell

OK. I can't access that either. I'm trying to solve that issue. Also, Please change file name A29507.CEMT_19.bam.ignore back to bam.