BSSeeker BSseeker2 issues

BSSeeker / BSseeker2

A versatile aligning pipeline for bisulfite sequencing data

http://pellegrini.mcdb.ucla.edu/BS_Seeker2/

MIT License

60 stars 25 forks source link

issues

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Pysam 0.11 align error

#50 desmodus1984 opened 5 months ago
0
Use .bam files generated with bwa-mem or re-make them?

#49 desmodus1984 opened 6 months ago
0
typo in README.md

#48 wbvguo opened 1 year ago
0
Determine unique mapped reads

#47 Hongxiang2023 opened 2 years ago
3
Compatibility with bismark?

#46 weishwu closed 2 years ago
2
[HELP] Unique mapped reads ratio

#45 hmyh1202 opened 2 years ago
2
[HELP] The output of bs_seeker2-call_methylation.py

#44 hmyh1202 opened 2 years ago
3
[help] How to speed alignment in BS-seeker2 ？

#43 hmyh1202 closed 2 years ago
6
How to re-run a interrupt job

#42 hcph opened 2 years ago
0
Why not move on to python 3 like every body else?

#41 marcovth opened 2 years ago
0
bs_seeker2-align.py: pysam ERROR

#40 ruih-ruih opened 2 years ago
1
Disclaimer for methylation call maximum methylation depth of 8000

#39 villars4 opened 3 years ago
1
outputs of bs_seeker2-build.py

#38 kwanghoon821 closed 3 years ago
2
Restart bs_align

#37 keckstrom opened 3 years ago
1
CGMap file the count of reads showing C or T here does not make scense

#36 salehsereshki opened 4 years ago
3
find multiple mapping region

#35 jeongmeani opened 4 years ago
1
How to handle data with replicates??

#34 AbRawoof opened 4 years ago
1
Understanding methylation C in mapped reads

#33 Surajuvm opened 4 years ago
0
'pysam.libcalignedsegment.PileupRead' object has no attribute 'qpos'

#32 joybio opened 4 years ago
0
Aligning pair end reads: IndexError: List index out of range.

#31 amitfenn opened 4 years ago
13
FAILED, ExitCode 1 in step #2 Map the reads

#30 christinalrichards opened 4 years ago
7
Adivce for preventing reverse compliment by bowtie2

#29 kscott94 opened 5 years ago
0
ERROR: Index DIR "_rrbs_150_400.." cannot be found in /home/knight05/software/BSseeker2-2.1.1/bs_utils/reference_genomes. Please run the bs_seeker2-build.py to create it with the correct parameters for -g, -r, --low, --up and --aligner.

#28 connorhknight closed 4 years ago
3
Error with python subprocess.py

#27 kscott94 closed 5 years ago
2
Excessive coverage in first 7000 positions in CGmap file

#26 Surajuvm closed 5 years ago
2
Only first three bases of aligned reads being used for methylation calling

#25 rjcorb closed 1 year ago
6
Randomly assigned

#24 olmath opened 5 years ago
3
Allow discordant mapping

#23 akramdi opened 5 years ago
7
Build Index Name Changed

#22 pzhang312 opened 5 years ago
1
Mappability decreased after version update.

#21 Moonju411 opened 5 years ago
1
Duplication

#20 hyystvar closed 5 years ago
1
Number of Cs reported in ATCGmap

#19 akramdi closed 5 years ago
4
Renaming Chromosomes in the wig file

#18 markmcdowall opened 5 years ago
4
Potential bias introduced by FilterReads.py

#17 yupenghe closed 6 years ago
3
Building Index WGBS Error

#16 bacantre opened 6 years ago
15
Dataset for testing

#15 bandapanda closed 5 years ago
2
bs_seeker2 align.py terminates after running for few minutes

#14 pkog opened 7 years ago
1
bs_seeker2-call_methylation.py line 286 makes bad comparison to pysam version string

#13 iankorf closed 7 years ago
3
Definition to the reads which are not fully converted by bisulfite treatment?

#12 Shicheng-Guo closed 7 years ago
1
bs_seeker2-call_methylation.py error report

#11 Shicheng-Guo closed 7 years ago
9
bs_seeker2-align.py and Cannot open input file

#10 Shicheng-Guo closed 7 years ago
1
Passing parameters to the pysam.sort()

#9 markmcdowall closed 7 years ago
3
Remove overlapped region between two mates for paired-end reads

#8 haodongchen closed 8 years ago
3
Base Qualities

#7 aheravi closed 7 years ago
3
pbat

#6 aheravi closed 7 years ago
1
Unique alignment

#5 buyejue closed 7 years ago
1
bs_seeker2-call_methylation.py has error with merged bam file

#4 hmkim closed 7 years ago
7
bs_seeker2-call_methylation.py has error with newest pysam

#3 najoshi closed 7 years ago
4
bs_seeker2-call_methylation.py generates wiggle file without header

#2 haodongchen closed 7 years ago
1
minor changes on bs_seeker2-align and bs_seeker2-build

#1 haodongchen closed 9 years ago
0