5 votes
Accepted

Kallisto error: index input file could not be opened!

Usually errors like these occur when an input file doesn't exist or is corrupt. But you might also see these errors if you don't have permissions to access the file for whatever reason. Although ...
Steve's user avatar
  • 3,079
3 votes

Kallisto psudoaligner quant not giving me expected output

As you surmised, kallisto requires a transcriptome fasta file, not a genome fasta file.
Devon Ryan's user avatar
  • 19.6k
3 votes

Kallisto RNA-seq errors because of incompatible indices when running <kallisto quant> using downloaded mouse index

It means that the version of the tool used for indexing and your current version are different and not compatible. Either downgrade your version to the version used for indexing, or build a new index ...
ATpoint's user avatar
  • 1,137
3 votes
Accepted

STAR quantMode vs RSEM vs Kallisto

STAR quantMode (GeneCounts) essentially provides the same output as HTSeq-Count would, ie. number of reads that cover a given gene. This is the most simple measure of expression you could get from RNA-...
DavyCats's user avatar
  • 487
2 votes

Error: FASTA file not found using building kallisto index

As mentioned in a comment, your working directory lacks the fasta file.
Devon Ryan's user avatar
  • 19.6k
2 votes

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

There has been a detailed comparison of kallisto and salmon for lncRNA transcripts by Zheng et al https://www.biorxiv.org/content/biorxiv/early/2018/01/09/241869.full.pdf It shows them to be near ...
Lior Pachter's user avatar
1 vote

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

I found a possible answer to my own question by reading this biostar page and also finding an NCBI page for downloading the reference genome file for viruses. You should go to this NCBI page and ...
Reza Rezaei's user avatar
1 vote

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

You might be interested in the viral sequence data from CATCH. There are various different viral subsets available. You could also try the NCBI virus website, filtering on human hosts. There's a "...
gringer's user avatar
  • 13.9k
1 vote

How to extract all sequences mapped to a transcript from Kallisto output

What Devon said. Alternatively, you could also just convert the bam to sam and then look for lines where the 3rd field (the reference the sequence is aligned to) is what you want: ...
terdon's user avatar
  • 9,856
1 vote
Accepted

How to extract all sequences mapped to a transcript from Kallisto output

Sort the BAM file again with samtools sort and then run samtools index on the result. That should fix the issue.
Devon Ryan's user avatar
  • 19.6k
1 vote

use Kallisto in galaxy

You have to click on the dropdown menu and select "Use transcriptome from history", which will allow you to specify your own file. I suspect the default will be built-in human transcriptome....
Kamil S Jaron's user avatar
1 vote

Files for paired end RNA sequencing

The problem is that the SRA website can be a little confusing. View the same project on ENA where the organization is more human-readable: https://www.ebi.ac.uk/ena/browser/view/PRJNA574273
burger's user avatar
  • 2,169
1 vote
Accepted

Strange p-value histogram for differential gene expression analysis

I found that using the Wald test instead of the Likelihood Ratio Test produced very different results with respect to the p-values. ...
James Hawley's user avatar
  • 1,384
1 vote

Strange p-value histogram for differential gene expression analysis

Try the protocol here for generating a different (smaller) dispersion estimate https://www.huber.embl.de/users/klaus/Teaching/DESeq2Predoc2014.html#inspection-and-correction-of-pvalues
swbarnes2's user avatar
  • 1,900

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