Hello everyone, I am new to bioinformatics and I am trying to use Kallisto for paired-end mapping. However, I got extremely low pseudoalignment rate for one paired end data and a high pseudoalignment rate for another data. Therefore, I was wondering what did i do wrong here:
kallisto quant -i Mus_musculus.GRCm39.cdna.all.index -o testoutputS71 --pseudobam 4wks_HFDWT_hepatocyte_8_S71_L003_R1_001.fastq.gz 4wks_HFDWT_hepatocyte_8_S71_L003_R2_001.fastq.gz
For the command above, I got: [quant] processed 41,296,205 reads, 8,393,745 reads pseudoaligned
However, for another data that with the command:
kallisto quant -i Mus_musculus.GRCm39.cdna.all.index -o testoutputS75 --pseudobam 16wks_HFDWT_hepatocyte_4_S75_L003_R1_001.fastq.gz 16wks_HFDWT_hepatocyte_4_S75_L003_R2_001.fastq.gz
For the 16wks data, I got: [quant] processed 34,437,268 reads, 22,243,785 reads pseudoaligned which is higher rate than the 4 wks data. Thank you so much for your help!
