Open
Conversation
… with QS statistics for CB/UMI read.
…r to define minimum seed length.
… calculated only for CB/UMI portions of the read (alexdobin#798).
…ns are output even of reads do not match genes.
…eatures GeneFull only option alexdobin#902
…olo count matrix from the BAM output.
…g-faults for --runMode soloCellFiltering runs.
…hen only EM options is specified in --soloMultiMappers.
…ntain NH and AS tags for duplication removal jobs (--runMode inputAlignmentsFromBAM --bamRemoveDuplicatesType UniqueIdenticalNotMulti).
…ranscriptomeSAM output that resulted in both mapped and unmapped output for some reads. Many thanks to Diane Trout (@caltech) for helping to track this bug.
…Features Gene and GeneFull were used together with --soloCBmatchWLtype 1MM_multi_pseudocounts option.
…eFull_CR counting. The results show better agreement with CR --include-introns option.
… implement BAM output for multimappers.
…trFeature=featureFirst.
…st feature on the list is used for GX,GN,XB,UB tags.
…mes for both unique- and multi-gene reads. Note that GX/GN tags are used to output gene ID/name for unique-gene reads.
…ches and one insertion+deletion for --soloType CB_UMI_Complex.
…e CB_samTagOut and --soloCBwhitelist None are used together.
…age in case the *true empty* cells cannot be found.
…e offending read number and line.
…dFilesIn, check every file for access.
…hat resulted in a seg-fault whem mapping to the rabbit genome. Issue alexdobin#1223: fixed the N_unmapped value reported in ReadsPerGene.out.tab. The single-end (i.e. partially mapped alignment are not excluded from N_unmapped. dev_EoI_2.7.9a_2021-09-30
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
8 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Only here to see all the changes so I could verify that 10XGenomics/orbit@f87846f would solve this issue.