Magdoll/cDNA_Cupcake
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
PythonBSD-3-Clause-Clear
Issues
- 0
collapse_isoforms_by_sam.py out of memory
#250 opened by SY348 - 2
- 3
fusion_collate_info.py KeyError: 'count_fl'
#240 opened by sonyuna90 - 3
ModuleNotFoundError: No module named 'cupcake.tofu' after installing cdna_cupcake in conda subenv
#246 opened by LilyLuyang - 0
cdna_cupcake与SQANTI3
#249 opened by tky199996 - 0
Demultiplex after clustering / genome alignment
#248 opened by davidvilanova - 1
Calling variants using IsoPhase from Iso-Seq data
#198 opened by Yexin-Zhang - 1
fusion_finder.py
#247 opened by tky199996 - 4
Script 'scripts/collapse_isoforms_by_sam.py' not found in metadata at '/research/rgs01/home/clusterHome/xchen2/software/cDNA_Cupcake/cupcake.egg-info'
#184 opened by xiaolongchen0627 - 0
Saturation analysis bug fixes; compatibility with newer isoseq cluster [make_file_for_subsampling_from_collapsed.py]
#244 opened by mrendleman - 0
solved
#242 opened by gengbaobao - 2
- 3
The question about finding fusion genes
#187 opened by 2209983424 - 1
setup.py requires sklearn instead of scikit-learn
#238 opened by cyrilcros - 3
collapse_isoforms_by_sam.py error TypeError: expected str, bytes or os.PathLike object, not NoneType
#180 opened by khandaud15 - 1
run_preCluster.py
#237 opened by jordur - 0
TypeError: iter_gmap_sam() got an unexpected keyword argument 'type' using collapse_isoforms_by_sam.py
#236 opened by gyorkeia - 2
pkg_resources.ResolutionError when running "collapse_isoforms_by_sam.py"
#220 opened by ssaif-cellarity - 0
- 0
lima for skera.bam
#234 opened by hmyh1202 - 3
- 0
Create sam format for collapse_isoforms_by_sam.py
#232 opened by rodrisenovilla - 4
cupcake2 directory missing, compilation fails
#231 opened by dvargaslandin - 0
chain_samples.py does not work!
#230 opened by unique379r - 7
No out put with get_abundance_post_collapse.py
#186 opened by B10inform - 0
- 0
Struggling in identifying the true positive fusion transcripts outputting from fusion_finder.py
#227 opened by wzhang42 - 0
How to configure the correct /optimal parameter and validate the true positive from PB fusion candidate list.
#226 opened by wzhang42 - 2
Where to find the demo data (input.fasta) used in fusion transcript finding (https://github.com/Magdoll/cDNA_Cupcake/wiki/Best-practice-for-fusion-transcript-finding)
#224 opened by wzhang42 - 1
collapse with some data was very slow
#209 opened by shizhuoxing - 1
Forward link display 404
#225 opened by wzhang42 - 0
demux_isoseq_with_genome.py Issue - expecting input not generated by get_abundance_post_collapse.py
#223 opened by KrRi4 - 0
Error about demux_isoseq_with_genome.py
#219 opened by Yuzhang0102 - 2
- 2
- 1
ISSUE: fusion_finder.py
#193 opened by tay45 - 1
Is there a hard limit on inter-exonic ranges?
#194 opened by markb729 - 0
Don't merge sample by chain_samples.py
#195 opened by 2209983424 - 2
Python version
#182 opened by tay45 - 0
chain_samples.py Exception: Sanity check failed!
#192 opened by tabeariepe - 1
problem using run_preCluster.py
#178 opened by jcleple33 - 1
- 2
MTX appears to have the wrong number of entries
#183 opened by nsalomonis - 1
little typo
#189 opened by splaisan - 1
- 0
- 1
- 1
collapse_isoforms_by_sam.py No module named 'cupcake.tofu.branch.c_branch'
#185 opened by kechalar-hua - 1
- 0
filter_away_subset.py problem
#174 opened by LileeGao