kallisto pseudoalignment rate is lower than literature


Hi guys,

Recently, I just beginning a new project about meta-analysis of RNA-seq.
The pipline that I choose is kallsito-tximport-WGCNA, but I just found my pseudoalignment rate is so low contrast to my reference(at the same pipline but I have more SRA files).

I just checked the possible reasons in biostars:1) different pipline generate different alignment rate; 2) trimmomatic may cause the lower alignment rate.

Therefore, I tried the Bowtie-Samtools pipline, kallisto from rawdata not do trimmomatic. However, these didn't work in my project.

Scince I have the reference literature, I thought the difference among us is the transcript index after re-checked it. But I can't understand if kallisto ignore the position of the reads compared to the genes, then the differences in transcripts should be mainly focused on the number of annotated genes. But the use of transcripts with a slightly lower number of genes should result in an acceptable comparison rate, instead of the difference between 1% and 50%.





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