DaehwanKimLab tophat issues

DaehwanKimLab / tophat

Spliced read mapper for RNA-Seq

http://ccb.jhu.edu/software/tophat

Boost Software License 1.0

90 stars 46 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

fix: AM_INIT_AUTOMAKE duplication error

#65 starsareintherose opened 12 months ago
0
bowtie1 failing with tophat v2.1.2

#64 kopardev opened 1 year ago
0
Fixing issue with newer automakes

#63 snehring opened 1 year ago
0
Compile issue

#62 BJWiley233 opened 3 years ago
2
Incorrect assignment of flag 0x2 (read mapped in proper pair)

#61 sam-israel opened 3 years ago
1
Different TopHat result between entire and subsampled fastq file

#60 ConcettaDe4 opened 4 years ago
0
tophat-fusion-post error when working with GRCh38

#59 byb121 opened 4 years ago
0
tophat_fusion_post value error GRCh38

#58 byb121 opened 4 years ago
0
Error with mapping colorspace reads

#57 galagoz opened 5 years ago
0
What's wrong with bowtie? (--reorder option with bowtie1)

#56 Damtagor opened 5 years ago
0
Score value

#55 SergejN opened 5 years ago
0
Clean up tophat's src/Makefile.am

#54 hartzell closed 6 years ago
4
Problem building w/ automake@1.16.1, with patch

#53 hartzell closed 6 years ago
4
Tophat Fusion Post error

#52 pbpayal opened 6 years ago
1
Fail to generate sam headers with bowtie1 >= v1.2

#51 ronin-gw opened 6 years ago
2
conflict between TopHat2.1.1 and HTSeq 0.9.1

#50 germaximus opened 6 years ago
0
Error locating program: samtools_0.1.18

#49 Arctictern6 opened 6 years ago
2
TopHat site is not reachable

#48 tushardave26 closed 6 years ago
1
tophat-2.0.14 :: tophat-fusion-post bad samtools call

#47 EricDeveaud opened 7 years ago
0
Do not double open genome fasta in gtf_to_fasta

#46 dondelelcaro closed 6 years ago
0
hg38 ensGene.txt.gz annotation has header line which needs to be removed

#45 komalsrathi opened 7 years ago
0
Uncaught exception of type St12out_of_range: basic_string::substr

#44 komalsrathi closed 7 years ago
1
Tophat 2.1.1 not compatible with bowtie2 v2.3

#43 rosbashlab opened 7 years ago
4
Uncaught exception of type St12out_of_range

#42 wookietreiber opened 7 years ago
2
The existing version fails on symlinks

#41 struckma opened 7 years ago
1
Fix lookup of bt2/bt2l files.

#40 elProxy closed 6 years ago
0
Tophat forces bowtie -k and -m to be equal

#39 brianpenghe opened 8 years ago
0
remove explicit make_pair template arguments

#38 wookietreiber opened 8 years ago
8
Configure issue when specifying --with-boost-thread

#37 miguelbernadi opened 8 years ago
0
Tophat v2.1.1 reports identical alignments and does not mark either as secondary.

#36 MatthewRalston opened 8 years ago
0
-G and -j option

#35 HaiHuaLiu opened 8 years ago
0
pythonmods intervaltree and sortedcontainers should install to site-packages, not bindir

#34 nieder opened 8 years ago
1
Makefile is not thread safe building prep_reads

#33 nieder opened 8 years ago
0
tophat2 file zero size

#32 gexijin closed 8 years ago
2
Missing alignments

#31 yevshin opened 8 years ago
0
Unit test

#30 mbparsa opened 8 years ago
0
tophat's help output lists obsolted link to manual

#29 mestia closed 8 years ago
1
Outdated link to manual in tophat.py usage error message

#28 sidney closed 8 years ago
0
Error: Could not find Bowtie index files /project/Ref_Genome/GRCm38.genome.fa.*.ebwt)

#27 52teth opened 8 years ago
0
equal_bam now checks if both alignments are to the same strand

#26 jeffhussmann closed 8 years ago
1
Incorrect MAPQ values reported when running with -G

#25 s-andrews opened 8 years ago
6
the autoconf report some error

#24 cdzhouzhiyuan opened 8 years ago
1
tophat2 uses relative path logic to find tophat executable...

#23 brazilbean closed 8 years ago
0
updated tarball (intervaltree, sortedcontainers), wrong install directory

#22 wookietreiber closed 8 years ago
1
Report Output Tracks Error

#21 msuperd1 opened 8 years ago
0
"Searching for junctions via segment mapping" slow with 1 million reads

#20 fcarelli opened 8 years ago
1
Compilation issues on some systems with Realtime extensions & fix

#19 philippbayer closed 8 years ago
1
tophat with -p > 1 results in missing reads

#18 jmack159 closed 8 years ago
8
Interoperability problems regarding read fields RNAME, RNEXT, POS and PNEXT for unmapped reads with mapped mate and MAPQ for all unmapped reads

#17 cbrueffer opened 8 years ago
0
Missing reads in accepted_hits.bam in some (as yet unknown) conditions

#16 cbrueffer opened 8 years ago
3