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Old 02-16-2015, 05:42 AM   #1
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Location: Oxford, UK

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Default Salmon and RSEM TPM estimate divergence?


I have been exploring which transcript quantification method to use for isoform level analysis. To date I have been performing gene level analysis with a STAR-htseqcounts-edgeR pipeline. However, I am now interested in quantifying isoform levels. To this end, I have mapped with STAR as before, but allowed the maximum number of reported mappings and reported out the transcriptome covering reads with the option available in the latest version of STAR. I have then used the default and appropriate read orientation settings for RSEM, salmon, and eXpress to see how much these tools agree with a single library of about 130million paired end human reads. When I compare the Salmon NumReads with either eXpress effective counts or RSEM estimated counts I find very good agreement with high Pearson correlation, (Salmon/RSEM read count figure attached) Although RSEM and Salmon are in much greater agreement linearly (Pearson correlation ~0.97 (RSEM/Salmon) vs ~0.70 (RSEM/eXpress, Salmon/eXpress), while Salmon reads are monotonically closer to eXpress values than RSEM ones (Spearman correlation ~0.92 (Salmon/eXpress) vs ~0.82 (Salmon/RSEM). However, it seems with Salmon and RSEM that both the FPKM, and more importantly, TPM values reported (another figure attached) disagree in a way that appears to be largely dependent on transcript length. Is there something in either model that significantly changes the way TPM is calculated to bias the transcript counts based on length when the read approximations produced by the two models are so similar? I wasn't able to identify such a bias from the documentation and literature.

I should say I do notice that RSEM tends to estimate much higher TPM than either eXpress or Salmon for transcripts around 100-200bp (read length is 51bp); however, the agreement with eXpress TPM values for anything larger than this is profound - while the Salmon and RSEM values diverge as a function of decreasing transcript length as seen in the second attached figure. Any discussion would be much appreciated.

Warm regards,
Attached Files
File Type: pdf Salmon_RSEM_isoform_read_counts_effect.pdf (4.75 MB, 25 views)
File Type: pdf RSEM_Salmon_TPM_length.pdf (4.60 MB, 22 views)
seversond12 is offline   Reply With Quote
Old 03-16-2015, 10:51 PM   #2
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Location: Phoenix, AZ

Join Date: Mar 2010
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What version of Salmon did you use? Have you posted to the google users board for sailfish/salmon? Rob is usually very good about getting answers to questions.

I agree with you somethings seems odd with the TPM values. Assuming this was done after the STAR alignments you are then just looking at the difference in the two programs. Perhaps there is a setting that is not performing as expected or not enabled by default. We noticed some odd behavior in salmon 2.7 when using stranded libraries but it tracked back to the command line implementation.
Jon_Keats is offline   Reply With Quote
Old 05-22-2015, 10:11 AM   #3
Location: Stony Brook, NY

Join Date: Aug 2013
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Hi seversond12,

I just came across this post. Did you ever track down the source of these differences? I'd be interested in knowing. Also, was this salmon result with / without bias correction?

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