IGV run batch

Question

[beaferbl]

Hi everyone! I'm trying to visualize a region on IGV loading a text file I've created to run in batch. With this file IGV loads the genome, goes to the position I want and takes an snapshot. However, it does not load the BAM files and the snapshots are not stored in the directory that I have specified. I can load the BAM files manually. So I think the problem is that IGV does not recognize the path to the files and folders. I tried to write the paths in two ways. (eg. C:/User/Desktop/file.bam and C:\User\Desktop\file.bam). I'm working in Windows. Does anyone have an idea? Thank you.

Answer 1

[Istvan Albert]

list the actual path in your post, C:/User/Desktop/file.bam would not be correct as it is missing the username

[beaferbl]

I wanted to simplify the example, but the username is also included in my path, it is C:/Users/username/Desktop/SRR8615343_X.bam. I wondered it there could be a problem with the slashes.

[Istvan Albert]

the reason the actual name is important is to see if you have spaces or other characters in the path that could complicate things

[beaferbl]

Hi Istvan, I eliminated the underlines and spaces and now it works. Thanks for your help!