• I’m having trouble with sleuth. Can I get help?
    • Yes. If you think you have discovered a bug that needs to be fixed please file a report on the GitHub page. If you have a question about installing or running the program, please ask on the kallisto-sleuth-users Google user group.
  • Where can I get announcements about new releases?
  • sleuth is spiffy but is it as accurate as other differential expression tools?
    • Yes. sleuth takes advantage of the boostraps of kallisto, thereby effectively leveraging technical replicates in the determination of differential expression. In the tests performed on both real and simulated data in the sleuth paper, we find that sleuth is more accurate than currently popular differential expression tools such as Cuffdiff2, DESeq2 and edgeR.
  • Can sleuth be used for quantifying abundances of transcripts or genes from RNA-Seq data?
    • No. sleuth is used after transcripts have been quantified using kallisto.
  • Is sleuth usable with both single-end and paired-end reads?
    • Yes.
  • Does sleuth require reads to be of the same length?
    • No.
  • Can sleuth be used to analyze single-cell RNA-Seq data?
    • Yes. However there are unique challenges in single-cell analysis that are not currently addressed by sleuth (but will be in the near future).
  • I’ve already mapped all my reads and counted the number of alignments to genes. Can I use those mappings with sleuth?
    • No. The mappings are not relevant and therefore cannot be used with sleuth.
  • Are you distributing transcriptomes for use with sleuth?
    • No. This is unnecessary because sleuth obtains transcript names from the kallisto quantification output.
  • My RNA-Seq was prepared with a stranded library. Is there a special option I need to use with sleuth?
    • No.
  • Is there a reason you picked the name sleuth for your program?
    • Yes.