Ecosyste.ms: Issues

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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

#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

#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

#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

#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

#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

#423 - Using kb to match the output of kallisto pseudo?

Issue - State: closed - Opened by stiv1n 8 months ago - 4 comments

#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

#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

#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

#386 - About the latest release

Issue - State: closed - Opened by chenrui333 over 1 year ago - 1 comment

#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

#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

#369 - Issues with chromosome file in kallisto

Issue - State: closed - Opened by st4302 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

#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