Kennedy-Lab-UW Duplex-Sequencing issues

Kennedy-Lab-UW / Duplex-Sequencing

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Empty output "SSCS.bam" (ConsensusMaker.py)

#57 Emily072020 closed 4 years ago
10
How to set --readlength while using ConsensusMaker.py

#56 Emily072020 closed 1 year ago
12
ConsensusMaker.py for Python3

#55 ni6o6 closed 4 years ago
1
problem with muts_by_read_position.py

#54 ron-geller closed 5 years ago
2
v3.1 Update

#53 bkohrn closed 4 years ago
1
ConsensusMaker.py - Little disagreement in defaults

#52 nanakiksc closed 4 years ago
1
ConsensusMaker.py error

#51 yanglq-bio closed 4 years ago
5
Add SRAFixer support for gzipped files and other SRRs. Reduce logging.

#50 susinmotion closed 7 years ago
0
Update docstring on tag_to_header.py to reflect new arguments

#49 susinmotion closed 4 years ago
1
Bug fix

#48 bkohrn closed 7 years ago
0
Fix error in UnifiedConsensusMaker

#47 bkohrn closed 7 years ago
0
How to account for upstream sample barcodes?

#46 dcraig2 closed 7 years ago
1
Fastq file has read bases as N

#45 abolia closed 7 years ago
4
Is the code for corrected_qual_score correct line 230 ?

#44 madsheilskov closed 4 years ago
1
AttributeError wtih pysam

#43 jpoell closed 7 years ago
2
UnifiedConsensusMaker.py IOError

#42 maoyibo closed 4 years ago
5
reduce speedup: list() 'in' is O(n), set() is O(1)

#41 aogier closed 7 years ago
2
Nh unpaired should not have mate flags

#40 nh13 closed 8 years ago
1
consensus_maker.py not identifying first read in sorted BAM

#39 noellenoyes closed 4 years ago
2
Revert "Nh duplex maker read order"

#38 scottrk closed 8 years ago
0
Flag should be 5 for unpaired reads (they are still paired, just this…

#37 nh13 closed 8 years ago
2
Nh duplex maker read order

#36 nh13 closed 8 years ago
0
Improvements to DuplexMaker and ConsensusMaker.

#35 nh13 closed 8 years ago
3
Revert "Remove output BAM from DuplexMaker and fixing up Docs."

#34 scottrk closed 8 years ago
0
Read name issues in ConsensusMaker.py and DulplexMaker.py

#33 nh13 closed 4 years ago
2
Remove output BAM from DuplexMaker and fixing up Docs.

#32 nh13 closed 8 years ago
0
Flag should be 5 for unpaired reads (they are still paired, just this…

#31 nh13 closed 8 years ago
5
Revert "The first tag was not being split correctly resulting in all unpaired"

#30 scottrk closed 8 years ago
1
Revert "Unpaired reads should still have their paired flag set."

#29 scottrk closed 8 years ago
0
Unpaired reads should still have their paired flag set.

#28 nh13 closed 8 years ago
2
The first tag was not being split correctly resulting in all unpaired

#27 nh13 closed 8 years ago
2
Ncutoff was always zero.

#26 nh13 closed 8 years ago
0
When using sam tags for the duplex sequences, remember to append the …

#25 nh13 closed 8 years ago
0
ConsensusMaker can read duplex tag sequences from a SAM tag (or tags).

#24 nh13 closed 8 years ago
7
Support gzip fastqs and specify tagstats output location.

#23 nh13 closed 8 years ago
1
PE_BASH_MAKER.py & bash_template.sh: --bwa option for aln or mem -T 1…

#22 jorgeboucas closed 7 years ago
1
Where can I find file "read_1.fq", "read_2.fq" ??

#21 lingbl closed 8 years ago
1
SRAFixer.py & Test_data_README

#20 jorgeboucas closed 8 years ago
0
mut-position.py

#19 zhangwl closed 4 years ago
3
Error with PE_BASH_MAKER.py

#18 KonstantinosC closed 4 years ago
15
ConsensusMaker.py

#17 zhangwl closed 8 years ago
9
Consensus maker

#16 arnavaz closed 4 years ago
16
ValueError quality and sequence mismatch: 76 != 59

#15 nordhuang closed 7 years ago
17
fqqq should be fq

#14 nordhuang closed 9 years ago
1
Update muts_by_read_position.py

#13 mwschmit closed 9 years ago
0
Error running CountMuts.py

#12 AmiDay closed 4 years ago
2
Update LICENSE

#11 mwschmit closed 9 years ago
0
fixed minor typos

#10 mwschmit closed 9 years ago
0
fixed minor typos

#9 mwschmit closed 9 years ago
0
fixed minor typos in the readme file

#8 mwschmit closed 9 years ago
0