Magdoll Cogent issues - Githubissues

Magdoll / Cogent

Coding Genome Reconstruction using Iso-Seq data

BSD 3-Clause Clear License

60 stars 17 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Scipy error when using process_kmer_to_graph.py script

#102 FarrahKhan1400 opened 2 years ago
0
get_bad_or_unmapped_hq.py

#101 NahlaHu opened 2 years ago
3
Sanity check failed by "filter_away_subset.py"

#100 unique379r opened 2 years ago
0
Should the fake genome be the reconstructed contigs + unassigned sequences + orphans?

#99 FarrahKhan1400 closed 2 years ago
0
run_preCluster.py --cpus=30 CalledProcessError(retcode, cmd)

#98 bijendrabio opened 2 years ago
1
When run collapse_isoforms_by_sam.py,it told me No valid records from my sorted.sam file

#97 wonitawowowo closed 2 years ago
3
Error in reconstruct_contig.py

#96 wonitawowowo closed 2 years ago
2
Error for reconstruct_contig.py

#95 zhuqianhua closed 3 years ago
2
Update README -- banner for Mar 2021 BFx Webinar

#94 Zuhayr-PacBio closed 3 years ago
0
First sequence in unassigned.list is formated wrong for get_seqs_from_list.py

#93 LionOfComarre opened 3 years ago
0
When running cogent, most of sequences ended up being in the tucked category

#92 mprotas69 opened 3 years ago
3
tally_Cogent_contigs_per_family.py error

#91 jodithea opened 3 years ago
0
Why happend this problem：pulp.apis.core.PulpSolverError: PuLP: Error while executing glpsol

#90 Gaodelike closed 1 year ago
1
Raise CycleDetectedException

#89 shri1984 opened 3 years ago
5
Add shebang

#88 tbertozzi closed 3 years ago
0
mash not found while running tests

#87 Luisitox closed 3 years ago
2
Failed reconstructions with highly repetitive gene family

#86 mollydawson closed 3 years ago
6
"segmentation error" running reconstruct_contig.py - version 6.1.0

#85 jcleple33 opened 4 years ago
8
"ARPACK error" during family finding on a large precluster bin

#84 jcleple33 closed 4 years ago
1
execution error with reconstruct_contig.py FileNotFoundError: [Errno 2] No such file or directory

#83 jcleple33 opened 4 years ago
4
bx-python error when install Cogent

#82 shenli-js closed 4 years ago
1
Will I able to run Cogent on RNAspades output?

#81 maorkn opened 4 years ago
2
Getting unassigned sequence IDs

#80 bruvellu opened 4 years ago
1
Should preCluster_out.tucked.fasta be included in the fake genome?

#79 bruvellu opened 4 years ago
0
process_kmer_to_graph.py conflicts with networkx 2.4

#78 Aprilcxy closed 4 years ago
1
BiopythonDeprecationWarning: This method is obsolete; please use str(my_seq) instead of my_seq.tostring().

#77 Yali1989 closed 4 years ago
1
Error because of bx-python==0.7.3

#76 jvhaarst closed 5 years ago
3
Use dependency versions that work with Python 2.7

#75 jvhaarst closed 5 years ago
0
failed reconstruction

#74 qiuxx221 closed 5 years ago
1
any eta for a python3 version?

#73 splaisan closed 4 years ago
4
Family Finding for a large dataset: run_mash.py, process_kmer_to_graph.py

#72 WallyL closed 5 years ago
5
Error when running filter_away_subset.py

#71 yiwenwang25 closed 5 years ago
2
splice_align.py: make alignment work in the EXPECTED_ERR_RATE == 0 case.

#70 cbrueffer closed 5 years ago
0
Install problem

#69 ClearloveMiao closed 5 years ago
1
Error when running get_abundance_post_collapse.py

#68 stanikae closed 5 years ago
1
generate_batch_cmd_for_Cogent_family issue

#67 qiuxx221 closed 5 years ago
3
Trouble in run_preCluster.py

#66 lijl459 closed 5 years ago
6
Error running collapse_isoforms_by_sam.py

#65 goodgodric28 closed 5 years ago
1
Solve attribute error, fixes #63

#64 jvhaarst closed 5 years ago
0
reconstruct_contig.py: Incompatible with python version 2.7.15

#63 AxelMacFoly closed 5 years ago
2
process_kmer_to_graph.py generating partitions of size 1

#62 goodgodric28 closed 5 years ago
1
Python encoding issue

#61 goodgodric28 closed 5 years ago
1
gmap_build failed

#60 MaPengyu closed 5 years ago
1
Segfault when running tutorial data

#59 monicabritton closed 4 years ago
5
Error while installing

#58 srbehera closed 4 years ago
2
More sequences after "Tutorial: Using Cogent to collapse redundant transcripts in absence of genome" ?

#57 jvhaarst closed 5 years ago
1
Change into directory for trimming.

#56 jvhaarst closed 5 years ago
0
Fixed typo.

#55 jvhaarst closed 5 years ago
0
interpreting the results

#54 ale07alvarez closed 5 years ago
2
reconstruct gene longer in 3 prime than associated isoforms

#53 jcleple33 opened 5 years ago
3