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83 Open 33 Closed
83 Open 33 Closed
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Issues list

Unusual behavior of cufflinks when a colon is present in the contig names
#138 opened Dec 15, 2023 by sarahfrail
# coverage and -g and -G
#137 opened Jun 27, 2023 by BGI2016
multithreading
#136 opened Jun 20, 2022 by denbogdan
cuffdiff error: number of labels must match number of conditions
#135 opened Apr 14, 2022 by Giuseppe1995
Cufflinks - Inconsistent Results for SAM/BAM File Sorted by Reference Position
#134 opened Oct 29, 2021 by CharlesARoy
Cuffmerge GTF error
#132 opened May 19, 2021 by nimishakbalan
cuffmerge
#131 opened May 13, 2021 by shainijoseph
Cuffmerge:ValueError: can't have unbuffered text I/O
#130 opened May 13, 2021 by shainijoseph
5
license clarification
#129 opened Mar 2, 2021 by rekado
Intron not within scaffold warnings
#128 opened Jun 27, 2020 by francicco
1
0 ReadHits still live
#126 opened Jan 30, 2020 by lijing28101
Nondeterministic segfault on OSX
#125 opened Dec 20, 2019 by ljyanesm
Correlation between replicates
#124 opened Dec 16, 2019 by aperreault
configure error: We could not detect the bam libraries
#121 opened Jun 21, 2019 by matteodelucchi
-m64 breaks build on architectures other than amd64
#119 opened May 29, 2019 by yurivict
Please add the corresponding ifdef for the code meant only for MinGW
#118 opened May 25, 2019 by yurivict
The https version of cufflinks website looks broken
#117 opened May 25, 2019 by yurivict
Please use std::fabs instead of just fabs in C++ to avoid conflicts
#116 opened May 25, 2019 by yurivict
warnings about parentheses, etc (clang-8)
#115 opened May 25, 2019 by yurivict
fatal error: 'boost/tr1/unordered_map.hpp' file not found
#114 opened May 25, 2019 by yurivict
CXXFLAGS should not be set to CFLAGS in configure
#113 opened May 25, 2019 by yurivict
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 opened Apr 29, 2019 by sourav8888
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 opened Apr 27, 2019 by thudxz
1
too many input files (limit set to 500 at compile time)
#110 opened Apr 25, 2019 by ZhuangZK
cufflinks gffread converts gff to gtf bug: missing specific transcript and gene name (gene0)
#109 opened Mar 1, 2019 by yuwenjiesail
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