Understanding tables in Altanlyze Results and Gene expression in control samples

[Brian Estevez]

Dear Altanlyze team,

I ran Altanylze on RNA SEQ FASTQ files from some control samples.

After analysis, I am confused about what these values actually mean. 

Could you help me understand what the values in the expression input file mean

In the EXP file, If gene A of sample 1 has a value of 182 what does that value mean?

What doe the values in the counts file mean? If gene A of sample 1 has 5,300 counts what does that mean? What are isocounts?

What do the valules in the transcript file mean?

In expression output file:

The same gene A in sample 1 when I open DATASET file has a different value than that shown in EXP file.

Also, why are the values in AVERAGE file the same as those in the EXP file?

Gene expression in control samples:

Finally, If not comparing to anything an I just want to know how much something is expressed in control samples is there an appropriate way to run the program.

Any help is very much appreciated.

Regards,

Brian

[Nathan Salomonis]

Hi Brian,

Let’s walk through these various values:

Isocounts = estimated number of reads for each transcript assigned through Kallisto to specific transcripts through an isoform graph-based approach (pseudo-aligned read counts from ker matches)

Expression file = non-log Kallisto transcript per million (TPM) estimates from pseudoalignment, which represent the sum of all transcript TPM values for that gene.

DATASET files = same as the expression file, but log2 normalized: log(TPM+1, 2) in excel or python math.log(TPM+1,2). A value of 1 is added to ensure the log2 transformed value is a minimum of 0 (log2 of 1 = 0).

Best,

Nathan

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