Questions tagged [kallisto]

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2answers
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How to get transcriptome FASTA file for viruses for Kallisto pseudo-alignment?

I guess the title is self-explanatory. I'd like to find the reference transcriptome files for a few human viruses. My RNA-seq samples are from human tumor cells that were infected with viruses. The ...
0
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1answer
30 views

Error: FASTA file not found using building kallisto index

I am trying to build an index on kallisto on mac using R studio and have saved my FASTA file to my desktop, however, when I run ...
0
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4answers
44 views

Files for paired end RNA sequencing

I am looking at the videos at a DIY Transcriptomics course and the speaker mentions that to run Kallisto for read alignment with paired end sequencing, one would enter the following: where the sample ...
2
votes
2answers
574 views

STAR quantMode vs RSEM vs Kallisto

I recently discovered this Snakemake pipeline for RNASeq that uses STAR's quantMode to quantify gene expression for DESeq2 differential expression analysis. In the past I've always seen the workflow ...
1
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2answers
241 views

Strange p-value histogram for differential gene expression analysis

I'm trying to perform pretty standard differential expression analysis using RNA-seq data. I've used Kallisto to perform RNA quantification and am using Sleuth to perform the differential expression ...
7
votes
1answer
459 views

Why are my kallisto and salmon results differing so much just for lncRNA transcripts?

I am running some analysis on an RNA-seq dataset. I have a list of transcripts that are potential lncRNA for which I ran both Kallisto and Salmon aligners. The input data for index building and ...