Hoohm dropSeqPipe issues

Hoohm / dropSeqPipe

A SingleCell RNASeq pre-processing snakemake workflow

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issues

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multiple cell barcodes

#121 ayyildizd opened 1 year ago
0
Fix: Temp in construction removed

#120 Hoohm closed 1 year ago
0
Add citation file for GitHub widget

#119 TomKellyGenetics closed 2 years ago
2
Error at perl locate

#118 amufaamo opened 2 years ago
0
SyntaxError in line 7 of Snakefile

#117 amufaamo closed 2 years ago
4
Error in rule repair

#116 Eigertje opened 2 years ago
0
Unsupported pickle protocol 5 in repair_barcodes.py

#115 PGuen opened 3 years ago
2
Also a problem with ViolinPlot

#114 ljouneau opened 3 years ago
0
ConvertToRefFlat fails while running Drop-seq_tools-2.4.0

#113 geshtin opened 3 years ago
5
create_star_index:

#112 jkubis96 closed 3 years ago
0
Less detected lncRNA

#111 YOU-k closed 4 years ago
1
CreateCondaEnvironmentException: Could not create conda environment from (env).yaml

#110 dgithub208 opened 4 years ago
0
Arabidopsis annotation missing transcipt_name

#109 vuzun opened 4 years ago
2
Issue with fastqc.smk

#108 rjg2186 opened 4 years ago
10
what strategy is applied to select CB

#107 YOU-k opened 4 years ago
1
Running dropSeqPIpe on 10X data

#106 suminwei2772 opened 4 years ago
1
10X split by oligos

#105 klevdiamanti closed 4 years ago
0
Query regarding ratio in config.yaml

#104 rjg2186 opened 4 years ago
0
help undestanding output

#103 RichardCorbett opened 4 years ago
13
unable to run conda as standalone application

#102 suminwei2772 opened 4 years ago
9
First test with Dolomite Nadia data

#101 RichardCorbett opened 4 years ago
9
10x v2 filter part in config.yaml

#100 YOU-k opened 4 years ago
2
Problem running the new version

#99 manarai opened 4 years ago
3
NH tag not found in BAM file

#98 abmmki closed 4 years ago
1
Doc update

#97 seb-mueller closed 4 years ago
3
Major overhaul of documentation towards version 0.6

#96 seb-mueller opened 4 years ago
2
migrate to Seurat version 3

#95 TomKellyGenetics closed 4 years ago
1
migrate to Seurat version 3

#94 TomKellyGenetics closed 4 years ago
7
migrate to Seurat version 3

#93 TomKellyGenetics closed 4 years ago
5
Fix numpy error calling multiQC

#92 TomKellyGenetics closed 4 years ago
9
Resolve issue with vioplot

#91 TomKellyGenetics closed 4 years ago
2
Problems when runing from conda env

#90 mcjmigdal opened 4 years ago
1
Another type of violin plot failure

#89 Hofphi opened 4 years ago
2
How are R1 reads filtered

#88 seb-mueller closed 4 years ago
1
Locus extraction for Introns

#87 JaydeepBhat closed 4 years ago
2
java.lang.OutOfMemoryError: GC overhead limit exceeded

#86 PGuen closed 5 years ago
2
No rule to produce meta

#85 abmmki closed 4 years ago
2
Genome not found, Picard's command line syntax is changing, violing plot not generated, expression.tsv not generated

#84 abmmki closed 4 years ago
8
violin plot fail

#83 terooatt opened 5 years ago
7
limitGenomeGenerateRAM=31000000000

#82 abmmki closed 5 years ago
3
KeyError for 'barcode-whitelist'

#81 abmmki closed 4 years ago
2
.snakemake/scripts folder is empty

#80 MarleyCodes opened 5 years ago
3
Shouldn't we correct cell-barcode errors before identifying core barcodes?

#79 dylkot opened 5 years ago
4
Problem creating refFlat

#78 Hofphi closed 4 years ago
6
Rerun with changed expected_cells in samples.csv requires remapping

#77 seb-mueller closed 4 years ago
4
Error in plot_yield, probably due to pigz bug in bbmap logs

#76 seb-mueller closed 5 years ago
4
fastqc not looking for adapters in the adapter file

#75 dylkot closed 5 years ago
6
sircel integration?

#74 colindaven closed 4 years ago
2
Insufficient memory for the Java Runtime Environment error

#73 seb-mueller closed 5 years ago
6
Hotfix/0.41

#72 seb-mueller closed 5 years ago
7