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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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Dear team,
I'm a little bit confused about the build index step. The manual says that it builds a transcriptome index but needs as input a genomic fasta and a gff. I would like to create the count…
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Hello, I am setting up FVE to run for the first time. Thank you for creating this program, I am excited about its utility! On my first attempt to run the test data set, I got this error:
(base) : …
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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
Dear all
I just found out that in commit https://github.com/nf-core/scrnaseq/commit/aae5fc5f618d1a4ccd40428d14050d838876f7fe we moved away from having ensembl_gene_ids a…
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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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From @cmeesters:
> [in ep03] we get to named in- and output without explaining the background or that in- and output are usually lists.
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Hello,
Thank you for keeping kallisto alive. These days, more and more I realise how its actually important and hard maintain and update tools across many years.
# Background:
I am processing …
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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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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…