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Hi,
I am following the getting started tutorial (http://pachterlab.github.io/kallisto/10xstarting.html) for single cell RNAseq but when I get to the point:
Download the “human-mouse” transcripto…
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Hello,
I am running Trinity through Docker and assembly went OK without any problems. But downstream analysis of abundances produces no output (I also don't get any errors). I am using this command:…
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### Description of feature
Universc is currently broken (it likely was for a while, because tests were running with the `-stub` option).
Prerequisite to make it work would be to finalize the modu…
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There was quite a few differences identified by looking at the barplots between kallisto's mapping (based on TPM data) and HTSEq mapping (based on Tophat2/HTseq). See the folder PredictorsDietInduced…
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Dear Laura,
There is a discrepancy between the gene count and transcript count from the count matrices generated by Kallisto. I generated the gene count matrix and tcc matrix from the same set of f…
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running:
kallisto quant -i transcripts.idx -o output833 --single -l 500 -s 50 SRR833_sub.fastq.gz
error:
...
[quant] finding pseudoalignments for the reads ...terminate called after throwing a…
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Hi,
i am trying your software on the kallisto branch (which seems very promising) and have a couple of questions:
- at the moment, the need to build and load in memory a kallisto index for train…
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Hi,
Since eXpress is not being maintained and kallisto is among the state-of-the-art transcript quantification tools, can kallisto output (quantified on transcript.fa) being support by KMA? Thanks.
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**Describe the issue**
I am executing this command as per 'box 2' in Nat. Biot. 2024 article:
~$ kb ref -i fpa_index.idx -g fpa_t2g.txt -f1 fpa_cdna.fasta cds_from_genomic.fasta genomic.gtf
**W…
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Hii Brain,
I hope you are doing well
I'm using the [align_and_estimate_abundance.pl](http://align_and_estimate_abundance.pl/) (alignment free abundance method through kallisto )
But I received t…