Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / pachterlab/kallisto issues and pull requests
#463 - lr-kallisto quant-tcc seg fault with bulk ONT
Issue -
State: open - Opened by sbresnahan 4 days ago
- 1 comment
#462 - Unable to retrieve spliced/unspliced RNA from single nuclei isolation
Issue -
State: closed - Opened by hyjforesight 13 days ago
- 1 comment
#461 - Devel
Pull Request -
State: closed - Opened by Yenaled 14 days ago
#459 - Kallisto Indexing runs but produces no data
Issue -
State: open - Opened by arese001 20 days ago
- 1 comment
#458 - Does kallisto bus in single cell mode (-x with anything not "bulk") turn off long read mode?
Issue -
State: closed - Opened by raysinensis 25 days ago
- 4 comments
#457 - lr-kallisto not producing hdf5 files for bulk long-read RNA seq data
Issue -
State: closed - Opened by apsteinberg about 1 month ago
- 3 comments
#456 - Using lr-kallisto for quantifying long-read bulk RNA-seq
Issue -
State: closed - Opened by alanlamsiu about 1 month ago
- 11 comments
#455 - About k-mer size
Issue -
State: closed - Opened by border-info-nt about 1 month ago
- 5 comments
#454 - related to: Illegal instruction error when running kallisto index
Issue -
State: open - Opened by molly-hetheringtonrauth about 2 months ago
- 7 comments
#453 - Can Kallisto align nucleotide sequences to protein database for calculating CPM
Issue -
State: open - Opened by xiaohong88999 2 months ago
- 1 comment
#452 - Effect of Kmer size on quantification
Issue -
State: open - Opened by Jayesh-Kumar-Sundaram 2 months ago
#451 - Distfile prefix changed for 0.51.0
Issue -
State: open - Opened by outpaddling 2 months ago
- 2 comments
#450 - lr-kallisto dorado unaligned bam files
Issue -
State: open - Opened by MustafaElshani 2 months ago
- 6 comments
#449 - Creating index for lrKallisto
Issue -
State: closed - Opened by ipatop 2 months ago
- 15 comments
#448 - lr-kallisto
Pull Request -
State: closed - Opened by Yenaled 2 months ago
#447 - kallisto ref died with <Signals.SIGILL: 4>.
Issue -
State: closed - Opened by yeroslaviz 3 months ago
- 5 comments
#446 - Behavior of kallisto quant with multiple lanes
Issue -
State: closed - Opened by rsiani 3 months ago
- 2 comments
#445 - Undocumented CPU Requirements?
Issue -
State: open - Opened by aralbright 3 months ago
- 1 comment
#444 - Getting isoform information from 10x 3' data with the --tcc option
Issue -
State: closed - Opened by BKover99 3 months ago
- 3 comments
#443 - Memory overflow with kb_ref
Issue -
State: closed - Opened by MartinezRuiz-Carlos 4 months ago
- 2 comments
#442 - Revert "Update batch processing length normalization to match non-batch processing length normalization"
Pull Request -
State: open - Opened by Yenaled 5 months ago
#441 - Update batch processing length normalization to match non-batch processing length normalization
Pull Request -
State: closed - Opened by bound-to-love 5 months ago
#440 - Kallisto index for ribo-depleted RNAseq libraries
Issue -
State: closed - Opened by MartinezRuiz-Carlos 5 months ago
- 5 comments
#439 - Support for SMART-Seqv4
Issue -
State: closed - Opened by cakeinspace 5 months ago
- 2 comments
#438 - I want to build an index with a geneses I have. Kallisto index errors out.
Issue -
State: closed - Opened by lcamVz 5 months ago
- 2 comments
#437 - Using kb-python for mars-seq
Issue -
State: open - Opened by sam-shariati 5 months ago
#436 - lr-kallisto, adding long read pseudoalignment and quantification options
Pull Request -
State: closed - Opened by bound-to-love 5 months ago
#435 - Question about kallisto indexes
Issue -
State: open - Opened by st4302 5 months ago
- 1 comment
#434 - kallisto gene vs transcript count
Issue -
State: open - Opened by Rajesh-HKU 6 months ago
- 4 comments
#433 - Feature request: Standalone pseudoalignment -> BAM output
Issue -
State: closed - Opened by bbimber 6 months ago
- 2 comments
#432 - Segmentation fault with kallisto quant
Issue -
State: closed - Opened by bbimber 6 months ago
- 4 comments
#431 - Facing issues while building on PPC64LE architecture.
Issue -
State: open - Opened by vinodk99 6 months ago
- 10 comments
#430 - Read-level pseudoalignment data that includes cellbarcode and UMI?
Issue -
State: closed - Opened by bbimber 6 months ago
- 6 comments
#429 - Error encountered when quantifying single-end reads with zero variance
Issue -
State: closed - Opened by MohHallal 7 months ago
- 2 comments
#428 - Kallisto handling multiple reads from single transcript?
Issue -
State: open - Opened by stromk 7 months ago
- 1 comment
#427 - Kallisto for Parsebio
Issue -
State: open - Opened by rootze 7 months ago
- 1 comment
#426 - building Index aborted
Issue -
State: closed - Opened by Himalayan-Java 7 months ago
- 2 comments
#425 - Kallisto abundance accuracy with pseudogenes
Issue -
State: closed - Opened by andrewxue98 8 months ago
- 2 comments
#424 - kallisto 0.50.1 fails with "Illegal instruction" when built on machines with AVX-512
Issue -
State: open - Opened by stianlagstad 8 months ago
- 2 comments
#423 - Using kb to match the output of kallisto pseudo?
Issue -
State: closed - Opened by stiv1n 8 months ago
- 4 comments
#422 - is it the 'clipped off poly-A tail' and 'clipped off poly-A tail' right?
Issue -
State: open - Opened by Bianzh1024 9 months ago
- 1 comment
#421 - Mapping kallisto equivalence classes to actual transcript sequences
Issue -
State: open - Opened by rubenchazarra 10 months ago
- 8 comments
#420 - kallisto quant 0.50.1 linux, illegal instruction
Issue -
State: open - Opened by deborah-chasman 10 months ago
- 1 comment
#419 - Kallisto total UMI difference between velocity and novelocity modes. (single cell)
Issue -
State: open - Opened by mortunco 10 months ago
- 4 comments
#418 - UMI count per transcript
Issue -
State: closed - Opened by MengjunWu 10 months ago
- 4 comments
#417 - estimate read counts of a specific region of a transcript
Issue -
State: open - Opened by zixuanxie 11 months ago
- 1 comment
#416 - Windows release not available for v0.50.1
Issue -
State: closed - Opened by GuyTeichman 11 months ago
- 2 comments
#415 - Change STORM-seq to uppper case for compatibility with kb_python
Issue -
State: open - Opened by genomics-kl 11 months ago
#414 - kallisto quant trying to allocate a huge amount of data
Issue -
State: closed - Opened by robert-player 11 months ago
- 2 comments
#413 - A few minor patches for portability
Issue -
State: open - Opened by outpaddling 11 months ago
#412 - D-list Usage Question
Issue -
State: closed - Opened by yvazirabad 11 months ago
- 2 comments
#411 - kallisto 0.50.0 can't index
Issue -
State: open - Opened by dariolez 11 months ago
- 14 comments
#410 - Build failure for v0.50.1 on macOS
Issue -
State: closed - Opened by p-linnane 11 months ago
- 12 comments
#409 - Devel
Pull Request -
State: closed - Opened by Yenaled 11 months ago
#408 - UMI count per gene
Issue -
State: open - Opened by tsofiya 11 months ago
- 8 comments
#407 - Add STORM- and VASA-seq support
Pull Request -
State: closed - Opened by biobenkj 11 months ago
#406 - Error message when using genomebam
Issue -
State: closed - Opened by olgabaranov 11 months ago
- 2 comments
#405 - Kallisto process killed or computer freezes while indexing
Issue -
State: open - Opened by hkarakurt8742 11 months ago
- 1 comment
#404 - D-list updates
Pull Request -
State: closed - Opened by Yenaled 12 months ago
#403 - Kallisto through Conda
Issue -
State: closed - Opened by ahmadalajami 12 months ago
- 2 comments
#402 - kallisto bustools vs. kb-python output differences
Issue -
State: closed - Opened by tsofiya 12 months ago
- 7 comments
#401 - un-aligned transcripts
Issue -
State: closed - Opened by tsofiya almost 1 year ago
- 7 comments
#400 - Incompatible indices error message seems to refer to incorrect version numbers
Issue -
State: open - Opened by jdreyf about 1 year ago
- 3 comments
#399 - Illegal instruction error when running kallisto index
Issue -
State: closed - Opened by nadjano about 1 year ago
- 12 comments
#398 - Kallisto bustools on single end Smart-seq3 data
Issue -
State: closed - Opened by kvn95ss about 1 year ago
- 2 comments
#397 - Kallisto not able to find the index file or abundance.tsv
Issue -
State: open - Opened by swinnier about 1 year ago
- 3 comments
#396 - does kallisto require unsorted reads?
Issue -
State: open - Opened by anoronh4 about 1 year ago
- 6 comments
#395 - All D-list transcripts have the same ID
Pull Request -
State: closed - Opened by kreldjarn about 1 year ago
#394 - conceptual question: assigning ambiguous reads to an isoform
Issue -
State: closed - Opened by saralinker about 1 year ago
- 3 comments
#393 - Added option to change d-list overhang
Pull Request -
State: closed - Opened by kreldjarn about 1 year ago
#392 - Documentation out of date
Issue -
State: open - Opened by mfansler about 1 year ago
- 3 comments
#391 - Easy fix for usage message
Issue -
State: closed - Opened by outpaddling about 1 year ago
- 1 comment
#390 - Segmentation fault writing pseudoalignments to BAM
Issue -
State: closed - Opened by ybao3 about 1 year ago
- 3 comments
#389 - EM priors
Pull Request -
State: closed - Opened by kreldjarn about 1 year ago
#388 - Automatically run tests once a week and for commits to src/** and test/**
Pull Request -
State: open - Opened by lauraluebbert over 1 year ago
#387 - Update KmerIndex.cpp so `--aa` option can handle lower case sequences
Pull Request -
State: closed - Opened by lauraluebbert over 1 year ago
#386 - About the latest release
Issue -
State: closed - Opened by chenrui333 over 1 year ago
- 1 comment
#385 - v0.50.0: Build failure related to bifrost-stamp not picking up zlib correctly
Issue -
State: closed - Opened by mjsteinbaugh over 1 year ago
- 4 comments
#384 - Devel
Pull Request -
State: closed - Opened by pmelsted over 1 year ago
#383 - Feature request: Add support for xz and zstd
Issue -
State: open - Opened by outpaddling over 1 year ago
#382 - Can't Bootstrap even after attempts to compile with cmake
Issue -
State: open - Opened by sikayler over 1 year ago
- 7 comments
#381 - Merging
Pull Request -
State: closed - Opened by Yenaled over 1 year ago
#380 - Quantify the expression of transposable elements
Issue -
State: closed - Opened by zhaotao1987 over 1 year ago
- 6 comments
#379 - Low number of reads pseudoaligned
Issue -
State: closed - Opened by ollieeknight over 1 year ago
- 1 comment
#378 - IDT Targeted Quantification
Issue -
State: closed - Opened by pintoa1-mskcc over 1 year ago
- 4 comments
#377 - Error: number of equivalence classes does not match index (kallisto quant-tcc)
Issue -
State: closed - Opened by shashkat over 1 year ago
- 5 comments
#376 - Why is there a big difference between kallisto and cellranger count result?
Issue -
State: open - Opened by aizhimin over 1 year ago
- 1 comment
#375 - Is it possible to create a pseudobam file with kallistobustools (kb)?
Issue -
State: open - Opened by aalajamii over 1 year ago
- 5 comments
#374 - No bus file created when no reads are pseudoaligned
Issue -
State: open - Opened by pmelsted over 1 year ago
#373 - how to gain raw counts for each gene ?
Issue -
State: closed - Opened by zhoudreames almost 2 years ago
- 3 comments
#372 - genomebam produces erroneous output for minus strand exons depending on order in gtf file
Issue -
State: open - Opened by SolKatzman almost 2 years ago
#371 - genomebam processing does not check for missing transcript_id
Issue -
State: open - Opened by SolKatzman almost 2 years ago
#370 - genomebam header does not contain sort_order value SO nor command_line CL
Issue -
State: open - Opened by SolKatzman almost 2 years ago
#369 - Issues with chromosome file in kallisto
Issue -
State: closed - Opened by st4302 almost 2 years ago
- 1 comment
#368 - Request: documentation of required gtf format for kallisto quant --genomebam option
Issue -
State: open - Opened by SolKatzman almost 2 years ago
- 5 comments
#367 - Request: clarification of interaction between quant options --pseudobam and --genomebam
Issue -
State: open - Opened by SolKatzman almost 2 years ago
- 1 comment
#366 - Request: release notes beyond v0.46.1
Issue -
State: open - Opened by SolKatzman almost 2 years ago
- 1 comment
#365 - libc++abi: terminating with uncaught exception of type std::length_error: vector/ using loompy to make loom file from fastq
Issue -
State: open - Opened by chousiniyade almost 2 years ago
- 2 comments
#364 - --chromosomes chrom.info
Issue -
State: closed - Opened by mapostolides almost 2 years ago
- 3 comments
#363 - Autoconf failure with MacOS
Issue -
State: closed - Opened by devang-mehta almost 2 years ago
- 3 comments