Can I run velocyto with RNAseq done with Illumina Hiseq

[Wanpeng-Wang]

Dear all,

I'm studying the germline cells and I isolated single nuclei from single germ cells and sequenced the content with Illumina Hiseq paired-end platform. The Nuclei are huge and gave me enough RNA content to make the libraries. I have 16 such samples/datasets with ~8Gbs of reads for each sample. Can I run velocyto with my data (maybe with run- Run on any technique)? I can use aligned and sorted bam files as input. Any suggestions in general? Any suggestions on reads alignment tool? Exon junction aware tools preferred?

Thanks!

Wanpeng

[Nithishwer]

Hey Wanpeng,

I am facing a similar situation. Did you have any progress with this?

Thanks, Nithish