Loading tsv/bam files in IGV - issue

[Marija Dacic]

Hello,

I have downloaded some ChIP-seq files from GEO Accession Viewer, and I'm attaching one here as an example, as well as the bam version of the same file obtained by deleting all but three columns.

The file doesn't give tracks when opened in IGV, as it as written as a tsv file. The file is shown below:

I have tried deleting all columns but "chr", "start" and "end" (along with column tiles), re-naming the file to .bam and opening, but I in that case I get an error that a file type cannot be determined.

My IGV version is 2.11.9, and my Mac OS is 11.2.3.

Thank you!

Regards,

Marija

[igv-help]

"tsv" just means the file is tab separated, it is not any specific format.   You will have to convert it to a supported file format, you can find a list in the user guide.    

The simplest format is probably "bed", which can be as little as 3 columns:  chr, start, and end.   If you convert to "bed", or any format, be sure to name the converted file with the proper extension. e.g.  ".bed".

[Marija Dacic]

Is there specific tool that needs to be used for the conversion? If I try just changing the extension, it doesn't not work - IGV isn't able to load the tracks. I tried reducing it to 3 columns and then changing to .bed ( as that is the simplest form), but it still did not work.

[James Robinson]

Did you save it as a plain text file (tab delimited)?  It's not going to work if you save it as an excel file.   

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[Marija Dacic]

When downloaded from GEO viewer it gets saved automatically to .tsv - which I know now is not a specific format, but what I did after is to just change the .tsv to .bed. There was no point at which I needed to pick between .txt or .xls.

[James Robinson]

Sorry I can't help you with these types of specifics,  you need to create a plain text tab-delimited file via some means with the 3 columns specified (at minimum).    There are many ways to do this.