Understanding tables in Altanlyze Results and Gene expression in control samples

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Brian Estevez

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Apr 20, 2019, 9:50:08 PM4/20/19
to Alternative Splicing and Functional Prediction
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

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Apr 20, 2019, 9:53:30 PM4/20/19
to Alternative Splicing and Functional Prediction
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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