Any easier way to deal with quant files generated by different versions of Salmon #705
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sykbod
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Hello,
I recently need to re-analyze RNAseq data from different experiments/batches. The quant files were generated with different versions of Salmon ( from 0.8.2 to 1.5.1) and that leads to errors when import data using tximport in DEseq2 later. The error message is
all(txId == raw[[txIdCol]]) is not TRUE
In addition: Warning message:
In txId == raw[[txIdCol]] :
longer object length is not a multiple of shorter object length
I guess that it is because the quant files from different samples had different numbers of rows. One experiment was generated with version 0.8.2 and others were generated with 1.3.1 and 1.5.1. Unfortunately, the original sequencing data from an experiment using version 0.8.2 was lost. So I was not able to redo Salmon for this experiment using the newer version of Salmon. I am wondering is there a way to convert/upgrade quant files to higher versions directly?
If not, I am considering using Salmon v0.8.2 to re-do all other samples. Hopefully not because the lower version is not as accurate as of the up-to-date version.
Thank you in advance for any advice!
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