Kallisto mapping paired end

Question

[Dk]

Hello everyone, I am new to bioinformatics and I am trying to map paired-end read with Kallisto. So I finished all the mapping with the reference transcriptomes with the command:

kallisto quant -i Mus_musculus.GRCm39.cdna.all.index -o testoutputS69 4wks_HFDWT_hepatocyte_5_S69_L003_R1_001.fastq.gz 4wks_HFDWT_hepatocyte_5_S69_L003_R2_001.fastq.gz

And I got three output files : abundances.h5, abundances.tsv, run_info.json. However, I realized that I need the BAM files too but I didn't add --pseudobam in previous command, so I was wondering is there anyway I can generate a BAM files for all of the files that I already generate before? Thank you so much!

Answer 1

[ATpoint]

Nope, rerun the entire command with that flag added. It's fast so it's not a big deal. Be aware that the BAM is transcriptome-space so it is not terribly useful anyway...

[Dk]

Thank youu!!