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Affects at least Themisto v2.1.0.
If the input multifasta file to `themisto build` contains a sequence with no nucleotides and the built index is used in the `pseudoalign` command, then the pseudoa…
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Problem: visualize the pseudoalignments: `kallisto quant -i transcripts.idx -b 30 -o kallisto_out --genomebam --gtf transcripts.gtf.gz --chromosomes chrom.txt reads_1.fastq.gz reads_2.fastq.gz`
Out…
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Hi, thanks for making this great tool!
It would be nice to know the fraction of the sample that could not be assigned to any target sequence. This would give an idea for how much of the sample is n…
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Hi,
Thank you for developing a tool that addresses the exploration of Isoform usage analysis. I want to give it a try to the tool, and at the beginning, I started with my own data using Kallisto p…
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### Description of feature
### Use Case:
It appears that at the moment the workflow must necessarily perform alignment, if `--skip_alignment` is true, then `--pseudo_aligner` must be populated wit…
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Dear Pachter team - first of all - thanks so much for providing such great tools for the community!
I have been using kb bustools on Google Colabs for several years now to align plate-based scRNA-s…
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**Describe the issue**
Is it possible to perform fragment length normalization for full-length UMI scRNA-seq data? I ask because I usually generate the TCC matrix and follow up with kallisto quant-tc…
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Hi,
I using kb to align my library with pre-built indexes, and analyzing it using transcript to genes file from the same source.
In a different issue I was told to use kallisto bus instead, so I bu…
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Thanks for making this useful tool!
I successfully used the distance tree workflow, but I struggle understanding how to generate the pseudoalignment (-a 'alignment.fasta' to be masked) in the ML tr…
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If pseudoalignments from paired reads are used as input and one or the other - for whatever reason - has differring number of alignments (reads) in it, mGEMS will exit with the error `Error: stoul exi…