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30 Open 81 Closed
30 Open 81 Closed
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Issues list

bowtie for short reads
#141 opened Jul 12, 2024 by alessandromacc
1
bowtie alignmnet produces sam bam files sizes for different fastq files
#140 opened May 24, 2024 by deepthi-omics
secondary alignment flag
#139 opened Oct 30, 2023 by adthrasher
Compatibility of Bowtie1 (v1.2.0 or later) with Tophat2
#138 opened Sep 4, 2023 by rason81
1
Is there an equivalent of "Bowtie2 --very-sensitive" for Bowtie1 [suggested label = Question]
#137 opened Mar 7, 2023 by AndreaMariani-AM
Cline paired 2 (fw:1, sam:1) test aborted with -Wp,-D_GLIBCXX_ASSERTIONS
#136 opened Feb 17, 2023 by junaruga
4
Some reference entries show up as duplicates
#135 opened Jul 13, 2022 by DeadlineWasYesterday
1
Questions about tracking the history of building index
#134 opened Jun 29, 2022 by Youpu-Chen
-m setting not outputting a sam file with an -NH tag
#133 opened May 20, 2022 by elayton13
Error: reads file does not look like a FASTQ file
#129 opened Feb 7, 2022 by amitjavilaventura
2
Bowtie no longer works with updated versions of tbb
#128 opened Jan 8, 2022 by ryandward
problem with option -n and -l
#126 opened Jul 21, 2021 by mewu3
Migrate Travis CI by May 31, 2021
#120 opened May 8, 2021 by junaruga
Bowtie: "Floating point exception: 8"
#118 opened Mar 10, 2021 by marcopann
1
Can bowtie accepts genomes higher than 3Gb for aligning?
#113 opened Jul 8, 2020 by AG-Run
Special characters in manual
#112 opened Jul 3, 2020 by BenLangmead
bowtie-build --debug --sanity crashes
#111 opened Jul 2, 2020 by BenLangmead
Code clean up?
#109 opened Apr 21, 2020 by mathog
@ch4rr0
4
The -m option only results in some "many mapped" reads being supressed
#94 opened Jul 11, 2019 by Riptides
@ch4rr0
Re-open issue: invalid fastq files produced using --un #8
#88 opened Nov 27, 2018 by elenichri
4
bowtie installation
#83 opened May 7, 2018 by VizeacoumarLab
1
-m and -M options don't make a difference
#82 opened Mar 22, 2018 by alj1983
7
Bowtie doesn't stop runing and return not complete alignment result!
#78 opened Jan 3, 2018 by kingdynasty
Compilation of Bowtie 1.2.2 with Intel 17.0.4 compatibility
#77 opened Dec 22, 2017 by marcc-hpc
@ch4rr0
9
Cannot compile with newer versions of C++ standard
#76 opened Dec 20, 2017 by cljacobs
1
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