SolKatzman issues

Results 7 issues of


                                            SolKatzman

How are indels, soft-clipping in CIGAR handled? Affected by read length?

Dear Yarden, These days, I use STAR for alignment, generally allowing it to specify soft-clipping, (S in the CIGAR field). A long time ago (Issue #16) it was stated "Most...

Request: documentation of required gtf format for kallisto quant --genomebam option

kallisto v0.48.0 The documentation for the kallisto quant --genomebam option states that a gtf file is required, but doesn't specify anything about the contents of that gtf file. For example,...

genomebam produces erroneous output for minus strand exons depending on order in gtf file

kallisto v0.48.0 I ran kallisto with the --genomebam option and supplied a gtf file that had lists of exons for various transcripts on the minus strand of the genome assembly....

genomebam processing does not check for missing transcript_id

kallisto v0.48.0 When run with the --genomebam option, kallisto requires a gtf file to map the coordinates of the exons for each transcript that is one of the targets in...

genomebam header does not contain sort_order value SO nor command_line CL

kallisto version v0.48.0 The header of the bam file created with the --genomebam option contains only these lines: `@HD VN:1.0` `@PG ID:kallisto PN:kallisto VN:0.48.0` `@SQ SN:chrIV LN:1531933` `...` I believe...

Request: clarification of interaction between quant options --pseudobam and --genomebam

kallisto v0.48.0 The documentation of the 2 kallisto quant options: --pseudobam and --genomebam is a bit ambiguous. a) are they mutually exclusive? If so an error should be thrown if...

Request: release notes beyond v0.46.1

On the download page there are no release notes beyond v0.46.1 from October 04, 2019. Latest download (as of December 5, 2022) using conda was v0.48.0, which seems to have...