search

pachterlab / kallisto

Near-optimal RNA-Seq quantification
https://pachterlab.github.io/kallisto
BSD 2-Clause "Simplified" License
658 stars 172 forks source link

Question about kallisto indexes #435

Open st4302 opened 7 months ago

st4302 commented 7 months ago

Hello,

I was wondering if it is more appropriate to use the v1 standard kallisto index https://github.com/pachterlab/kallisto-transcriptome-indices/releases for bulk RNA seq data compared to an index created by concatenating Mus_musculus.GRCm39.cdna.all.fa.gz Mus_musculus.GRCm39.ncrna.fa.gz and then using kallisto index on that file.

I know the v1 kallisto index was created using kb ref but I am not using kb ref for alignment. The command that I will be using to align will be kallisto quant -i mousecdna_ncrna -o mouse_kallisto/MTKO5 -t 4 --rf-stranded MTKO5_R1_001.fastq.gz MTKO5_R2_001.fastq.gz

I am interesting in lncRNAs for my project.

Thank you

Yenaled commented 7 months ago

You can use the prebuilt indices (they contain lncRNA targets and kb ref uses “kallisto index” under the hood anyway). However, if you use those, make sure you’re using the latest version of kallisto (0.50.1).

st4302 commented 2 months ago

Is it ok to use the same prebuilt index for data where I only expect to have coding genes?

Thank you

Yenaled commented 2 months ago

Yes