tecangenomics nudup issues

tecangenomics / nudup

NuDup -- Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.

http://www.tecangenomics.com

GNU Lesser General Public License v3.0

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issues

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wrong entry - sorry

#25 martinheine closed 3 years ago
1
How to get index.fq file from bcl files?

#24 YuanTian1991 closed 4 years ago
1
fix output shorten qname in --rmdup-only mode

#23 frankyan opened 5 years ago
0
shorten qname in output bam file in --rmdup-only mode

#22 frankyan opened 5 years ago
2
Guidance on aligner.

#21 mlovci closed 5 years ago
0
more descriptive error messages when samtools isn't in $PATH?

#20 andrewejaffe opened 5 years ago
0
sort: ... disorder: ... Error

#19 boro2013 closed 5 years ago
7
nudup instances loop endlessly when run in parallel inside a container

#18 AdrianS85 opened 5 years ago
2
Better description on how to append tag to read name (Case 2)

#17 cjfields closed 5 years ago
5
Not valid Read FASTQ File, ill-formatted Index sequences, possibly spaces

#16 sklages closed 6 years ago
2
I have a few nugen processed paired end human samples. I processed the bam files from HiSeq using the following pipeline. Fastqc>Trim>Tophat>Sort>NugenDedup.py>Htseqcounts. But I am getting 0 counts for a couple of my samples after I ran nugen Deup scirpt..Without dedup I have more counts..but is it possible to get 0 counts..isn't dedup supposed to remove only the PCR duplicates?

#15 pbpayal closed 6 years ago
2
fix typo cmd to cmds

#14 shuelga closed 6 years ago
0
[ ERROR] - global name 'cmd' is not defined

#13 yongchao closed 6 years ago
2
Enhancement request: better error reporting when BAM file contains supplementary alignments

#12 lparsons opened 6 years ago
3
correct 18bp in descriptions to be 16bp

#11 shuelga closed 6 years ago
0
Broken pipe?

#10 FabianGrammes opened 7 years ago
7
Which output file from nudup.py to use with bismark_methylation_extractor?

#9 ghost closed 7 years ago
1
Fix to allow relative temp directory specifications

#8 lparsons closed 7 years ago
0
PrepDeDupPairedEnd bug fix

#7 l337x911 closed 7 years ago
0
SAM Error

#6 bimbam23 closed 7 years ago
1
Version 2.3

#5 l337x911 closed 7 years ago
0
Added bioconda-badge

#4 lparsons closed 7 years ago
0
Add tags for new release versions

#3 lparsons closed 7 years ago
0
nudup invalid syntax error

#2 amitgsir closed 7 years ago
1
Paired end deduping fails instantly

#1 mjafin closed 8 years ago
4