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36 Open 11 Closed
36 Open 11 Closed
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Issues list

bowtie1 failing with tophat v2.1.2
#64 opened Oct 6, 2022 by kopardev
Compile issue
#62 opened Dec 3, 2020 by BJWiley233
2
Incorrect assignment of flag 0x2 (read mapped in proper pair)
#61 opened Oct 18, 2020 by sam-israel
1
Different TopHat result between entire and subsampled fastq file
#60 opened Jun 24, 2020 by ConcettaDe4
tophat-fusion-post error when working with GRCh38
#59 opened Oct 9, 2019 by byb121
tophat_fusion_post value error GRCh38
#58 opened Jul 24, 2019 by byb121
Error with mapping colorspace reads
#57 opened Apr 9, 2019 by galagoz
What's wrong with bowtie? (--reorder option with bowtie1)
#56 opened Dec 12, 2018 by Damtagor
Score value
#55 opened Nov 7, 2018 by SergejN
Tophat Fusion Post error
#52 opened Feb 26, 2018 by pbpayal
1
Fail to generate sam headers with bowtie1 >= v1.2
#51 opened Jan 24, 2018 by ronin-gw
2
conflict between TopHat2.1.1 and HTSeq 0.9.1
#50 opened Dec 19, 2017 by germaximus
Error locating program: samtools_0.1.18
#49 opened Nov 21, 2017 by Arctictern6
2
tophat-2.0.14 :: tophat-fusion-post bad samtools call
#47 opened Jun 6, 2017 by EricDeveaud
hg38 ensGene.txt.gz annotation has header line which needs to be removed
#45 opened Mar 17, 2017 by komalsrathi
Tophat 2.1.1 not compatible with bowtie2 v2.3
#43 opened Feb 15, 2017 by rosbashlab
4
Uncaught exception of type St12out_of_range
#42 opened Sep 22, 2016 by wookietreiber
2
Tophat forces bowtie -k and -m to be equal
#39 opened Jun 4, 2016 by brianpenghe
Configure issue when specifying --with-boost-thread
#37 opened Apr 25, 2016 by miguelbernadi
Tophat v2.1.1 reports identical alignments and does not mark either as secondary.
#36 opened Apr 24, 2016 by MatthewRalston
-G and -j option
#35 opened Apr 16, 2016 by HaiHuaLiu
pythonmods intervaltree and sortedcontainers should install to site-packages, not bindir
#34 opened Apr 6, 2016 by nieder
1
Makefile is not thread safe building prep_reads
#33 opened Apr 6, 2016 by nieder
Missing alignments
#31 opened Mar 15, 2016 by yevshin
Unit test
#30 opened Feb 23, 2016 by mbparsa
ProTip! no:milestone will show everything without a milestone.