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Can we add support for storing and printing the input file names (and their colors) to the next version that touches the index format? Fulgor for example has a `print-filenames` subcommand that we cou…
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We have download many metagenome fastq files and need to align them to a custom protein database for calculating CPMs. We use 'kaliisto index --aa' command to build index from our FASTA-file contain…
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Hi!
Many thanks for all you development efforts!
I have six data sets that I would be interested in benchmarking with Kallisto-bustools, however I just found out that kalllisto bus only suppor…
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When trying to get pesudobam file, it gives me the core-dump error.
Machine is Ubuntu server with x86-64 architecture.
```
kallisto quant -i Trinity.fasta.kallisto_idx -l 590 -s 160.95 -o out --pseu…
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hi there, a bit confused about the input to this, particularly the --ref setting
are these to be the same genomes used to perform pseudoalignment on, or? are they supposed to be bins?
sorry if i…
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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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Dear @alexdobin
This is not an issue but rather asking your thoughts about recent manuscripts about splice/unsplice/ambiguous read classification. I am sure you are reading on this but havent seen …
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Hello,
I'm interested in visualizing read distribution for specific cells/clusters from scRNAseq data. Is there a method to generate a pseudoalignment bam/sam file from kb outputs to view via IGV? …
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[per Marcel Schilling]
Add comma separators to numbers greater than 999. E.g:
> [index] k-mer length: 31
> [index] number of targets: 193,761
> [index] number of k-mers: 120,402,343
> [index] number…
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Hello,
I am getting an error while indexing of the BAM files. I have installed the tool using conda. So the kallisto version is at 0.44 as mentioned. Below is STDOUT
```
Results stored in: stra…