Hi, Im completely new to analysis of seq data. Additionally, am completely new to using code of any kind so its all a bit of a struggle....
I've been provided with mapped sequencing files in .sop format from BGI (ChIP-seq). All I want to do for now is be able to view a file in IGV... So far I've used a perl script to convert the .sop to a .sam. I tried opening the .sam in IGV but it said it needs to be indexed and wouldn't open. Aside from this others have suggested converting to bam as this would be a more manageable file size. I've downloaded samtools and think I have this running. I've put my .sam file into the samtools folder and used the following command
$ view -b -S file.sam > file.bam
But keep getting
Vim: Warning: Output is not to a terminal
After which the terminal locks up and I have to close it.....
Any help or other suggestions would be greatly appreciated.....
I've been provided with mapped sequencing files in .sop format from BGI (ChIP-seq). All I want to do for now is be able to view a file in IGV... So far I've used a perl script to convert the .sop to a .sam. I tried opening the .sam in IGV but it said it needs to be indexed and wouldn't open. Aside from this others have suggested converting to bam as this would be a more manageable file size. I've downloaded samtools and think I have this running. I've put my .sam file into the samtools folder and used the following command
$ view -b -S file.sam > file.bam
But keep getting
Vim: Warning: Output is not to a terminal
After which the terminal locks up and I have to close it.....
Any help or other suggestions would be greatly appreciated.....
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