Salmon auxiliary output

Question

[g.wang2]

Hi All,

I'm unsure how to view the *.gz files (e.g. fld and biases files) in the "aux_info" folder after running Salmon. After unzip the .gz files, they are still not in human readable format. Is another tool required to access these files? Any suggestions are appreciated.

Thanks Guan

[mcsimenc]

@Ahill I tried encoding these auxiliary files in ASCII format using the base64 module from Python and the resulting encoding is not what the file is described as containing in the salmon docs. For example, the fld file is documented as containing integer counts, but when I encode it as ASCII using base64.b64encode() the result is only letters, i.e AAAAA...

Answer 1

[Ahill]

See the Salmon docs: here. These are gzipped, but in a binary format which the docs describe. Based on a quick look at the descriptions, it appears you could get the contents of these files by reading the uncompressed contents and decoding them using binary constructs available in many scripting languages like Python, Perl, or R.