Magdoll SQANTI2 issues - Githubissues

Magdoll / SQANTI2

SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3

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error using GFF or converted GTF

#71 noor-albader opened 3 years ago
1
Recurring perl errors - gmst.pl

#70 anilkanthi closed 3 years ago
7
Gene_IDs in GTFs

#69 moschmi closed 4 years ago
3
issue with python=3.7

#68 adeslatt closed 3 years ago
0
sqanti_filter.py

#67 moschmi closed 4 years ago
4
Error with sqanti_qc2.py command

#66 tfiskur closed 4 years ago
4
FileNotFoundError: missing refAnnotation_***.genePred file?

#65 rebailey closed 4 years ago
3
_corrected.gtf file without transcript line

#64 yemao701 opened 4 years ago
4
Problem running with cage_peak

#63 PJ-Shaw closed 4 years ago
2
About adapting SQANTI2 to process transcripts from nanopore cDNA sequencing

#62 yjx1217 closed 4 years ago
2
python 3.7 bx-python error

#61 mmarchin closed 4 years ago
1
How to utilize sqanti2 classification result for genome optimizaion?

#60 leosfan opened 4 years ago
1
Isoform class transcript distribution versus rarefaction curve

#59 pcarbone closed 4 years ago
1
sqanti2_qc.py fails with assertion error

#58 vkkodali closed 4 years ago
6
Tamma Collapse for 5' cap selected samples

#57 BeatrizdeToledo opened 4 years ago
1
Possible error from input gff files instead of fasta/fastq/gtf files

#56 leosfan closed 4 years ago
10
gene_id annotation

#55 morellr closed 4 years ago
2
Assertion Error

#54 HegedusB closed 4 years ago
7
isoform map to scaffold which without reference gene

#53 shenli-js opened 4 years ago
1
input isoforms.fasta for chain_samples.py

#52 pcarbone closed 4 years ago
4
Error during Isoform Classification

#51 aarzalluz closed 4 years ago
4
python: can't open file 'sqanti_qc2.py': [Errno 2] No such file or directory

#50 laguda-1996 closed 4 years ago
2
Existing files from "incomplete" runs cause errors on subsequent runs

#49 wolfgangrumpf closed 4 years ago
1
SQANTI qc is very slow

#48 gmstanle closed 4 years ago
2
[v5.1.0] Error: invalid feature coordinates (end<start!)

#47 yejilee-biostat closed 4 years ago
4
Half of the HQ isoforms are classified as antisense and NIC

#46 qoiopipq closed 4 years ago
7
error in --is_fusion

#45 prometheusloong closed 4 years ago
3
How to generate a short read expression file?

#44 qoiopipq closed 4 years ago
1
python2 and python3 hybird ?

#43 EXGDT closed 4 years ago
1
SQANTI2 fails at ORF finding

#42 wolfgangrumpf closed 4 years ago
11
More specific instructions installing cDNA_cupcake

#41 astrophys closed 4 years ago
1
sqanti_filter2.py is not working

#40 tay45 closed 4 years ago
2
for duplicated read names -> having "dup" on gtf output, but not on SAM/FASTA output

#39 yejilee-biostat opened 4 years ago
11
Support SAM/BAM input for SQANTI2

#38 Magdoll opened 4 years ago
0
Could I use BAM as input rather than FASTQ?

#37 juheon closed 4 years ago
1
AssertionError on sqanti_qc2.py v4.0 and cDNA_Cupcake v8.5

#36 huyuem closed 4 years ago
5
Error in sqanti_qc2.py

#35 psur9757 opened 4 years ago
12
A question about "associated_gene" from _classification.txt

#34 yejilee-biostat closed 4 years ago
2
Adding a version check.

#33 mhsieh closed 4 years ago
0
Error when running SQANTI2

#32 Treywea closed 5 years ago
2
will SQANTI2 works on custom fasta file?

#31 LuyiTian closed 5 years ago
3
subprocess.CalledProcessError in PERL

#30 yzhang88 opened 5 years ago
3
Possibility for Nanopore data

#29 josiegleeson closed 5 years ago
1
some Questions about the results

#28 shangguandong1996 closed 5 years ago
1
subprocess.CalledProcessError

#27 tay45 closed 5 years ago
11
Caution: long input filenames create unrelated error messages

#26 markb729 closed 5 years ago
3
AttributeError running squanti2

#25 qoiopipq closed 5 years ago
2
KeyError in sqanti_qc2.py version 3.5

#24 defendant602 closed 4 years ago
7
AssertionError on v3.3

#23 defendant602 closed 5 years ago
1
TypeError on v3.2

#22 kiekyon closed 5 years ago
2