Is there Quality score/measure to compare salmon results using different kmer values?

Question

[karni_bedirian]

Dear Biostar community,

Is there quality control measure/score so that I can compare my output of Salmon using different kmer values? I have about 54 bp reads and have used kmer 31,29,27,25,... I would like to know if there is a QC measure/score so that I can know which kmer value to use?

I have looked ad the mapping rates, but it seems it does not tell a significant difference between different kmer values.

Thanks in advance, Karni

Answer 1

[ATpoint]

The kmer length is not too much of a factor given it is shorter than the read length in my experience. I did a small test a while back, see Salmon Quantification for RNA-seq Read Pairs with Different Lengths and the influence of different lengths is minor. It all comes down to the libary quality. In sloppy language: If the sample is crap, so will be the mapping/quantification. The important factor is that the library is good quality and read length is sufficient. Therefore, decide for a kmer length, e.g. 25 and use it for your analysis.

[karni_bedirian]

Hi,

Thank you for your response. So I can conclude that there is no QC score to evaluate my results, am I right?

[ATpoint]

Not that I know of.

[karni_bedirian]

okay thank you, appreciated!