cole-trapnell-lab cufflinks issues

cole-trapnell-lab / cufflinks

Boost Software License 1.0

307 stars 116 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Unusual behavior of cufflinks when a colon is present in the contig names

#138 sarahfrail opened 7 months ago
0
# coverage and -g and -G

#137 BGI2016 opened 1 year ago
0
multithreading

#136 denbogdan opened 2 years ago
0
cuffdiff error: number of labels must match number of conditions

#135 Giuseppe1995 opened 2 years ago
0
Cufflinks - Inconsistent Results for SAM/BAM File Sorted by Reference Position

#134 CharlesARoy opened 2 years ago
0
Performance data of cufflinks in computing speed.

#133 guoqiangqi closed 2 years ago
0
Cuffmerge GTF error

#132 nimishakbalan opened 3 years ago
0
cuffmerge

#131 shainijoseph opened 3 years ago
0
Cuffmerge:ValueError: can't have unbuffered text I/O

#130 shainijoseph opened 3 years ago
5
license clarification

#129 rekado opened 3 years ago
0
Intron not within scaffold warnings

#128 francicco opened 4 years ago
1
Fix the 'thread' C++ ambiguity by changing to boost::thread.

#127 yurivict opened 4 years ago
0
0 ReadHits still live

#126 lijing28101 opened 4 years ago
0
Nondeterministic segfault on OSX

#125 ljyanesm opened 4 years ago
0
Correlation between replicates

#124 aperreault opened 4 years ago
0
error: reference to 'thread' is ambiguous

#123 yurivict closed 4 years ago
1
Fix build on Ubuntu 19.04

#122 smowton closed 5 years ago
0
configure error: We could not detect the bam libraries

#121 matteodelucchi opened 5 years ago
0
updated download link of test data

#120 matteodelucchi opened 5 years ago
0
-m64 breaks build on architectures other than amd64

#119 yurivict opened 5 years ago
0
Please add the corresponding ifdef for the code meant only for MinGW

#118 yurivict opened 5 years ago
0
The https version of cufflinks website looks broken

#117 yurivict opened 5 years ago
0
Please use std::fabs instead of just fabs in C++ to avoid conflicts

#116 yurivict opened 5 years ago
0
warnings about parentheses, etc (clang-8)

#115 yurivict opened 5 years ago
0
fatal error: 'boost/tr1/unordered_map.hpp' file not found

#114 yurivict opened 5 years ago
0
CXXFLAGS should not be set to CFLAGS in configure

#113 yurivict opened 5 years ago
0
Getting warning while using cuffnorm - "Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct parameters (--frag-len-mean and --frag-len-std-dev) be provided."

#112 sourav8888 opened 5 years ago
0
configure: error: We could not detect the bam libraries. Try installing htslib or libbam, or specifying a path to one with --with-bam=/some/path

#111 thudxz opened 5 years ago
1
too many input files (limit set to 500 at compile time)

#110 ZhuangZK opened 5 years ago
0
cufflinks gffread converts gff to gtf bug: missing specific transcript and gene name (gene0)

#109 yuwenjiesail opened 5 years ago
0
Make `cuffmerge` Python 3 compatible

#108 chenghlee opened 5 years ago
0
Tweak `unordered_map.hpp` include for newer Boost releases

#107 chenghlee opened 5 years ago
0
cufflinks not working on 150bp PE?

#106 tanpuekai opened 5 years ago
1
build failure biascorrection.h:18:10: fatal error: boost/tr1/unordered_map.hpp: No such file or directory

#105 greyltc opened 5 years ago
2
The test data url is invalid

#104 LucaMarconato opened 5 years ago
0
cuffmerge invalid syntax

#103 Juliajuli opened 5 years ago
5
Can I change the tracking id ?

#102 Leehyeonjin93 opened 6 years ago
0
Can cufflinks report FPKM for chimeric transcripts/gene fusions?

#101 geekgeekhello opened 6 years ago
0
installation error cufflinks

#100 hemantgujar opened 6 years ago
0
Cufflinks installation error on hpc

#99 hemantgujar closed 6 years ago
0
Issue loading reference annotation

#98 NBaileyNCL closed 6 years ago
2
max-bundle-frags does NOT work?

#97 wangyugui closed 6 years ago
1
Cuffdiff bug: FPKM is way above range conf_lo to conf_hi (and is wrong)

#96 sammyjava opened 6 years ago
1
segment when cufflinks with -mask-file

#95 wangyugui opened 6 years ago
1
CPM(counts per M reads) for cuffdiff --max-bundle-frags will be better when different seq depth?

#94 wangyugui opened 6 years ago
2
Add Htslib support

#93 smowton closed 6 years ago
0
How to create an Ubuntu 17.04 Singularity container with cufflinks installed?

#92 eriksjolund opened 6 years ago
0
print --help to stdout instead of stderr

#91 eriksjolund opened 6 years ago
1
Cuffcompare: Transcripts with FPKM=0 and FPKM_conf_hi >0

#90 tlaguna opened 6 years ago
0
cufflinks fails to build from source with GCC-7

#89 mestia closed 6 years ago
3