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 ...
- 3,297
3
votes
Kallisto psudoaligner quant not giving me expected output
As you surmised, kallisto requires a transcriptome fasta file, not a genome fasta file.
- 19.8k
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 ...
- 1,511
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-...
- 507
2
votes
Error: FASTA file not found using building kallisto index
As mentioned in a comment, your working directory lacks the fasta file.
- 19.8k
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 ...
- 21
2
votes
problem with running Kallisto on single cell data
created another environment called "kb", where I installed Kallisto-bustools
This is known to work well. What about installing bustools in the same env as Kallisto?
Alternatively you can ...
M__♦
- 13k
1
vote
problem with running Kallisto on single cell data
Well, it's embarassing to say but...I didn't have Autotools, CMake, and Make installed! Once I installed them, I could run the command. However, I am running now in another problem: even though the ...
- 39
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 ...
- 169
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 "...
- 15.1k
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:
...
- 10.6k
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.
- 19.8k
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....
- 5,652
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
- 2,209
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.
...
- 1,394
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
- 2,061
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