BenLangmead bowtie issues

BenLangmead / bowtie

An ultrafast memory-efficient short read aligner

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issues

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bowtie alignmnet produces sam bam files sizes for different fastq files

#140 deepthi-omics opened 1 month ago
0
secondary alignment flag

#139 adthrasher opened 8 months ago
0
Compatibility of Bowtie1 (v1.2.0 or later) with Tophat2

#138 rason81 opened 10 months ago
1
Is there an equivalent of "Bowtie2 --very-sensitive" for Bowtie1 [suggested label = Question]

#137 AndreaMariani-AM opened 1 year ago
0
Cline paired 2 (fw:1, sam:1) test aborted with -Wp,-D_GLIBCXX_ASSERTIONS

#136 junaruga opened 1 year ago
4
Some reference entries show up as duplicates

#135 DeadlineWasYesterday opened 1 year ago
1
Questions about tracking the history of building index

#134 Youpu-Chen opened 2 years ago
0
-m setting not outputting a sam file with an -NH tag

#133 elayton13 opened 2 years ago
0
Remove '.' from include path search.

#132 tjni opened 2 years ago
0
Fix compilation on arm64.

#131 tjni opened 2 years ago
0
Bowtie not mapping 100%

#130 Stakaitis closed 2 years ago
1
Error: reads file does not look like a FASTQ file

#129 amitjavilaventura opened 2 years ago
2
Bowtie no longer works with updated versions of tbb

#128 ryandward opened 2 years ago
0
XM:i SAM Optional field ... seems like hits + 1 for all hits?

#127 MikeAxtell closed 2 years ago
3
problem with option -n and -l

#126 mewu3 opened 2 years ago
0
-M option reports the wrong number of reads processed

#125 dominik-handler closed 2 years ago
2
Bowtie hangs when running on very large genomes

#124 ferayd closed 2 years ago
8
Mismatch flag

#123 KONeill872 closed 3 years ago
0
bowtie install error on Apple M1

#122 hidvegin closed 2 years ago
1
Website updates

#121 BenLangmead opened 3 years ago
0
Migrate Travis CI by May 31, 2021

#120 junaruga opened 3 years ago
0
bowtie 1.3.0 generated sam files error

#119 hidvegin closed 3 years ago
11
Bowtie: "Floating point exception: 8"

#118 marcopann opened 3 years ago
1
What is the sense of third_party/cpuid.h

#117 tillea closed 2 years ago
2
scripts/tests/large_idx.py: #! python -> python3

#116 smoe opened 3 years ago
0
DeprecationWarning: the imp module is deprecated

#115 junaruga closed 3 years ago
2
s390x/ppc64le: bt2_locks.h: Error: Unrecognized opcode: `pause'

#114 junaruga closed 2 years ago
6
Can bowtie accepts genomes higher than 3Gb for aligning?

#113 AG-Run opened 4 years ago
0
Special characters in manual

#112 BenLangmead opened 4 years ago
0
bowtie-build --debug --sanity crashes

#111 BenLangmead opened 4 years ago
0
Install bowtie

#110 paolabc closed 2 years ago
1
Code clean up?

#109 mathog opened 4 years ago
4
bowtie-align-l-debug fail

#108 bensonlew closed 4 years ago
0
Unmapped reads not suppressed using --no-unal and possibly wrong stderr stats

#107 bepoli closed 3 years ago
2
SeqAn license info is not enough?

#106 junaruga closed 3 years ago
4
Update to seqan 1.4.2

#105 junaruga closed 3 years ago
3
Invalid double quote character is used in the code

#104 junaruga closed 3 years ago
3
bowtie reports incorrect result when using bowtie2 index

#103 qifei9 closed 2 years ago
3
Add aarch64, ppc64le and s390x cases to Travis CI

#102 junaruga closed 3 years ago
16
Renaming the v1.2.3 src archive to "bowtie-1.2.3-src.zip"?

#101 junaruga closed 2 years ago
4
Missing newlines in --max and --un output files

#100 ferayd closed 3 years ago
18
Allow to override build date and host

#99 bmwiedemann closed 3 years ago
1
Get decoded content of index files

#98 lazovicff closed 4 years ago
1
Please update scripts using python to python3

#97 mestia closed 2 years ago
1
Axolotl genome index building with Bowtie 1.2.3

#96 Gil-marquez closed 2 years ago
3
Makefile alphabet.cpp

#95 xusailor opened 4 years ago
4
The -m option only results in some "many mapped" reads being supressed

#94 Riptides opened 4 years ago
0
bowtie with recent SeqAn

#93 mestia closed 2 years ago
3
Bowtie clips read before matching

#92 ferayd closed 5 years ago
4
Extremely low mapping rate using D. melanogaster, Flybase, r5.22 genome index

#91 ruochenj closed 5 years ago
1