timoast/sinto issues and pull requests

#71 - filterbarcodes --barcode_regex returns ls

Issue - State: closed - Opened by ewholling 5 months ago - 1 comment

#70 - fragments command instantly completes, no errors, blank output

Issue - State: closed - Opened by mousepixels 7 months ago - 1 comment

#69 - filterbarcodes cell file format

Issue - State: closed - Opened by cathalgking 8 months ago - 1 comment

#68 - sinto filterbarcodes too many temp files

Issue - State: closed - Opened by cathalgking 8 months ago - 6 comments

#67 - Gzipped barcode file loading

Issue - State: closed - Opened by jonathangriffiths 10 months ago - 1 comment

#66 - Is the bam filtered by barcodes still sorted?

Issue - State: closed - Opened by jase11 10 months ago - 1 comment

#65 - fix NoneType errors

Pull Request - State: closed - Opened by bgruening 11 months ago - 1 comment

#64 - SInto pipeline

Issue - State: closed - Opened by hesbornomwandho 12 months ago - 1 comment

#63 - Unable to run

Issue - State: closed - Opened by GuiSeSanz about 1 year ago - 6 comments

#62 - Sinto Fragments Output Empty

Issue - State: closed - Opened by Tripfantasy over 1 year ago - 4 comments

#61 - Specify a whitelist when adding barcodes

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

#60 - Fuzzy barcode processing

Issue - State: closed - Opened by dawe over 1 year ago - 4 comments

#59 - For single end bam file

Issue - State: closed - Opened by yoshihiko1218 over 1 year ago - 1 comment

#58 - sinto filterbarcodes Remote I/O error

Issue - State: closed - Opened by 23Niklas almost 2 years ago - 1 comment

#57 - Error "No space left on device"

Issue - State: closed - Opened by NGroen over 2 years ago - 1 comment

#56 - collapsing reads issue follow-up

Issue - State: open - Opened by rtyags over 2 years ago

#55 - filterbarcodes drops unmapped reads

Issue - State: closed - Opened by joycekang over 2 years ago - 6 comments

#54 - keeping unmapped reads in filterbarcodes

Issue - State: closed - Opened by anthonybejjani over 2 years ago - 1 comment

#53 - Potential naming issue with import of importlib-metadata package

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

#52 - Key Error 'RG' with filterbarcodes

Issue - State: closed - Opened by alwhiteh over 2 years ago - 8 comments

#51 - Modified RG tag and duplicated entry after sinto

Issue - State: closed - Opened by Zepeng-Mu over 2 years ago - 6 comments

#50 - details of filtering

Issue - State: closed - Opened by rtyags over 2 years ago - 1 comment

#49 - Too many open files

Issue - State: closed - Opened by nitinnarwade over 2 years ago - 4 comments

#48 - collapsing reads

Issue - State: closed - Opened by rtyags almost 3 years ago - 3 comments

#47 - scaling with bam size and parallel processing

Issue - State: closed - Opened by rtyags almost 3 years ago - 4 comments

#46 - error parsing barcode from middle of read name with nametotag

Issue - State: closed - Opened by jkgrenier almost 3 years ago - 5 comments

#45 - error filterbarcodes with 10x ATAC bam

Issue - State: closed - Opened by LiNk-NY almost 3 years ago - 2 comments

#44 - error reading barcodes file with `read_cell_barcode_file`

Issue - State: closed - Opened by LiNk-NY almost 3 years ago - 2 comments

#43 - Single cell RNA seq: cellranger BAM file split by filtered cell barcode as separate file

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

#42 - Single-Read BAM compatibility

Issue - State: closed - Opened by macros29 almost 3 years ago - 2 comments

#41 - Samtools is not a dependency

Issue - State: closed - Opened by macros29 about 3 years ago - 5 comments

#40 - Regarding utils::chunk_bam()

Issue - State: closed - Opened by hukai916 about 3 years ago - 2 comments

#39 - How to deal with the same barcodes when merging the bam files from multiple samples?

Issue - State: open - Opened by zhanglab2008 about 3 years ago - 1 comment
Labels: enhancement

#38 - sinto filterbarcodes error - OSError: truncated file

Issue - State: closed - Opened by onionpork about 3 years ago - 3 comments

#37 - Move cell barcode from name to bam tag

Issue - State: closed - Opened by hukai916 over 3 years ago - 2 comments
Labels: enhancement

#36 - Why collapsing reads across cell barcode?

Issue - State: closed - Opened by hukai916 over 3 years ago - 4 comments

#34 - python

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

#33 - Configurable fragment +/- shift

Issue - State: closed - Opened by suragnair over 3 years ago - 4 comments

#32 - Fragments file has size of zero

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

#31 - Missing Fragments edge case

Issue - State: closed - Opened by suragnair over 3 years ago - 4 comments

#30 - Error with addtags on a transcriptome-aligned BAM file

Issue - State: closed - Opened by austin-abbvie over 3 years ago - 5 comments

#29 - Sinto fragments: negative positions in output

Issue - State: closed - Opened by cflerin almost 4 years ago - 3 comments

#28 - Empty bam fles after merging in filterbarcodes

Issue - State: closed - Opened by anamariaelek almost 4 years ago - 4 comments

#27 - filterbarcodes - Samtools merge failed

Issue - State: closed - Opened by rb56 almost 4 years ago - 2 comments

#26 - sinto installation - problem with python

Issue - State: closed - Opened by mirifax almost 4 years ago - 2 comments

#25 - sinto bam filement returning a empty fragment filement

Issue - State: closed - Opened by qiuqin-wu about 4 years ago - 3 comments

#24 - sinto filterbarcodes returning empty bams

Issue - State: closed - Opened by debbie28 about 4 years ago - 2 comments

#23 - Memory issue with Add cell barcodes to FASTQ read names function

Issue - State: closed - Opened by baigal628 about 4 years ago - 3 comments

#22 - empty fragment file

Issue - State: closed - Opened by rojinsafavi over 4 years ago - 5 comments

#21 - no fragments produced

Issue - State: closed - Opened by rojinsafavi over 4 years ago - 5 comments

#20 - Zero-length fragments generated from Cell Ranger BAM

Issue - State: closed - Opened by cflerin over 4 years ago - 4 comments

#19 - Citing Sinto

Issue - State: closed - Opened by DrDrLitte over 4 years ago - 1 comment

#18 - Filterbarcodes issues

Issue - State: closed - Opened by rb56 over 4 years ago

#17 - filter barcodes parallel issue

Issue - State: closed - Opened by Pentayouth over 4 years ago - 4 comments
Labels: bug

#16 - filterbarcodes bam outputs very small?

Issue - State: closed - Opened by Annika18 over 4 years ago - 3 comments

#15 - filter barcodes parallel issue

Issue - State: closed - Opened by omansn over 4 years ago - 1 comment

#14 - Use SAM/BAM opening idiom recommended by pysam

Pull Request - State: closed - Opened by winni2k over 4 years ago - 1 comment

#13 - Add tagtotag. Closes #12

Pull Request - State: closed - Opened by winni2k over 4 years ago - 3 comments

#12 - Renaming read tags

Issue - State: closed - Opened by winni2k over 4 years ago - 2 comments

#11 - filterbarcodes TypeError: unhashable type: 'list'

Issue - State: closed - Opened by Brawni over 4 years ago - 3 comments

#10 - Add tagtorg command

Pull Request - State: closed - Opened by winni2k almost 5 years ago - 2 comments

#9 - filterbarcodes empty BAM file

Issue - State: closed - Opened by Brawni almost 5 years ago - 7 comments

#8 - Do you accept PRs?

Issue - State: closed - Opened by winni2k almost 5 years ago - 2 comments

#7 - issue running filterbarcodes

Issue - State: closed - Opened by tagaler almost 5 years ago - 4 comments

#6 - Error running filterbarcodes

Issue - State: closed - Opened by DrDrLitte almost 5 years ago - 2 comments

#5 - Normalizing the signal - creating a bigwig

Issue - State: closed - Opened by gouthamatla almost 5 years ago - 2 comments

#4 - Filter cell barcodes from BAM file using read tag other than "CB"

Issue - State: closed - Opened by liaojinyue almost 5 years ago - 1 comment

#3 - Update to v0.3

Pull Request - State: closed - Opened by timoast almost 5 years ago

#2 - Clarifications

Issue - State: closed - Opened by Connorr0 about 5 years ago - 1 comment

#1 - Update docs

Pull Request - State: closed - Opened by timoast over 5 years ago

GitHub / timoast/sinto issues and pull requests