Swart-lab bleties issues

Swart-lab / bleties

IES retention analysis from PacBio CCS reads

https://swart-lab.github.io/bleties

MIT License

4 stars 2 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

MILRET muscle version number regexp returning error

#29 gh-ecs closed 2 years ago
1
Retention scores systematically underestimated

#28 kbseah opened 3 years ago
0
Multi-segment CDS entries not handled by Insert module

#27 kbseah closed 3 years ago
1
Milraa string index out of range

#26 mohamma1 closed 3 years ago
6
Document attributes fields in comment header of GFF3 output

#25 kbseah opened 3 years ago
0
Document change in TA-boundary coordinate reporting in v0.1.9

#24 kbseah opened 3 years ago
0
Refactor feature tables to use python numbering internally exclusively

#23 kbseah opened 3 years ago
0
Change `ta_pointer_start` and `ta_pointer_end` reporting

#22 kbseah opened 3 years ago
0
MILRAA reports wrong retention score for fuzzy length matches

#21 kbseah closed 3 years ago
0
MILRAA report deletions for subreads

#20 kbseah opened 3 years ago
0
MILCOR and MILTEL for subreads

#19 kbseah opened 3 years ago
0
Mask selected regions in MILRAA

#18 kbseah opened 4 years ago
0
Milraa failed in subread mode

#17 kbseah closed 4 years ago
1
Bin reads by mapping to transcriptome

#16 kbseah opened 4 years ago
0
Report paths of external programs used to log

#15 kbseah closed 4 years ago
0
Option to run MILTEL only on part of alignment

#14 kbseah closed 4 years ago
0
Distinguish subread vs ZMW coverage with MILRAA subread mode

#13 kbseah closed 4 years ago
1
Report "breakage score" for MILTEL

#12 kbseah closed 4 years ago
0
Identify potential rearrangements

#11 kbseah opened 4 years ago
0
Visualize correlations in retention between IESs in same contig

#10 kbseah opened 4 years ago
0
Handle temp files with `tempfile`

#9 kbseah closed 4 years ago
0
Select region from BAM file to analyse

#8 kbseah closed 4 years ago
0
Insert module to insert putative IES sequences

#7 kbseah closed 4 years ago
1
Compress MILCOR fasta output bins

#6 kbseah opened 4 years ago
0
Parallelize IES reporting in fuzzy mode

#5 kbseah opened 4 years ago
2
Check for BAM index and exit gracefully if absent

#4 kbseah closed 4 years ago
0
Order of execution of MILRET

#3 gh-ecs closed 4 years ago
3
Could the minimum default length for identifying a candidate IES by MILRAA (25 bp) be reduced?

#2 gh-ecs closed 4 years ago
3
"Junction" in MILRAA gff3 output clashes with "junction" from mapped reads

#1 gh-ecs closed 4 years ago
6