OceanGenomics/mudskipper issues and pull requests

#44 - Unable to run with spatial bam

Issue - State: open - Opened by chrisquatjr 3 months ago

#43 - No mapped read in output bam with gff file

Issue - State: open - Opened by steven-bioinfo 6 months ago

#42 - Error in reading annotation file.

Issue - State: closed - Opened by anoronh4 11 months ago - 2 comments

#41 - print statements

Pull Request - State: closed - Opened by TejasTemker about 1 year ago

#40 - quantification and correlation script

Pull Request - State: closed - Opened by TejasTemker over 1 year ago - 2 comments

#39 - comments

Pull Request - State: closed - Opened by TejasTemker over 1 year ago - 1 comment

#38 - Api comments

Pull Request - State: closed - Opened by TejasTemker over 1 year ago

#37 - comments

Pull Request - State: closed - Opened by TejasTemker over 1 year ago

#36 - test case

Pull Request - State: closed - Opened by TejasTemker over 1 year ago - 1 comment

#35 - assertion failure: last>=first

Issue - State: open - Opened by lkmack21 over 1 year ago - 2 comments

#34 - Differences in quantification when using transcriptome BAM from Muskipper or STAR

Issue - State: open - Opened by osvaldoreisss almost 2 years ago

#33 - cargo build --release!

Issue - State: closed - Opened by Samaneh14 about 2 years ago - 5 comments

#32 - Support for overhang alignment

Pull Request - State: closed - Opened by yfei-w about 2 years ago - 2 comments

#31 - Clippy clean

Pull Request - State: closed - Opened by rob-p about 2 years ago

#30 - Better temp file management during shuffle

Pull Request - State: closed - Opened by sjbaker47 about 2 years ago

#29 - fix issue #24

Pull Request - State: closed - Opened by gmarcais over 2 years ago - 5 comments

#28 - Fix for test_bam2bam

Pull Request - State: closed - Opened by HosseinAsghari over 2 years ago

#27 - Change libradicl link to a new repo

Pull Request - State: closed - Opened by opplatek over 2 years ago - 1 comment

#26 - Does this pull request fix issue #24 ?

Pull Request - State: open - Opened by jelber2 over 2 years ago - 8 comments

#25 - test_bam2bam fails

Issue - State: closed - Opened by rob-p over 2 years ago - 2 comments
Labels: bug

#24 - 'main' panicked at 'index out of bounds: the len is 1 but the index is 1'

Issue - State: open - Opened by aleighbrown over 2 years ago - 22 comments

#23 - Compile errors

Issue - State: open - Opened by jdidion over 2 years ago - 6 comments

#22 - Shuffle

Pull Request - State: closed - Opened by sjbaker47 over 2 years ago - 6 comments

#21 - Compiling error on MacOS

Issue - State: closed - Opened by jianshu93 over 2 years ago - 3 comments

#20 - Adding more tags required for salmon bulk analysis

Pull Request - State: closed - Opened by haghshenas over 2 years ago

#19 - Update README.md

Pull Request - State: closed - Opened by rob-p over 2 years ago

#18 - Build a unmapped barcode frequency table

Issue - State: open - Opened by haghshenas over 2 years ago
Labels: enhancement

#17 - Multiple bugfixes

Pull Request - State: closed - Opened by haghshenas almost 3 years ago

#16 - Let the user choose the path for the GTF index

Issue - State: closed - Opened by haghshenas almost 3 years ago
Labels: enhancement

#15 - Recover cell barcode if it contains a single N only

Issue - State: open - Opened by haghshenas almost 3 years ago - 2 comments
Labels: enhancement

#14 - BAM record is not updated properly for reverse orientation transcripts

Issue - State: closed - Opened by haghshenas almost 3 years ago
Labels: bug

#13 - Properly set the flag for secondary alignments

Issue - State: open - Opened by haghshenas almost 3 years ago - 4 comments
Labels: bug

#12 - Disagreement with the annotation when there is a spliced alignment

Issue - State: closed - Opened by haghshenas almost 3 years ago
Labels: bug

#11 - Initial implementation of shuffle command

Pull Request - State: closed - Opened by sjbaker47 almost 3 years ago - 4 comments

#10 - Support overhanging alignments

Issue - State: open - Opened by haghshenas almost 3 years ago
Labels: enhancement

#9 - Off by one error in setting the number of threads

Issue - State: open - Opened by haghshenas almost 3 years ago
Labels: enhancement

#8 - Negative coordinate in output BAM

Issue - State: closed - Opened by haghshenas almost 3 years ago - 1 comment
Labels: bug

#7 - Handle unmapped reads more properly

Issue - State: closed - Opened by haghshenas almost 3 years ago
Labels: bug

#6 - Reading from SAM with multiple threads

Issue - State: open - Opened by haghshenas almost 3 years ago
Labels: bug

#5 - Dropping some alignments against overlapping transcripts

Issue - State: open - Opened by haghshenas almost 3 years ago
Labels: bug

#4 - Inconsistent CIGAR strings

Issue - State: closed - Opened by haghshenas almost 3 years ago - 1 comment

#3 - Wrong pairing of alignments

Issue - State: closed - Opened by haghshenas almost 3 years ago
Labels: bug

#2 - Supporting supplementary alignments

Issue - State: closed - Opened by haghshenas almost 3 years ago - 1 comment
Labels: enhancement

#1 - Output RAD format from mudskipper for bulk (both SE and PE) and single-cell

Pull Request - State: closed - Opened by haghshenas almost 3 years ago - 6 comments

GitHub / OceanGenomics/mudskipper issues and pull requests