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• bowtie2 error while mapping the fastq files ?
  I am trying to map fastq files by using bowtie2 and the command i am using is: bowtie2 -q -x ./In...
• bowtie-2 build error
  Hi All I am trying to build bowtie index, on Windows 10 using CygWin. Getting the following erro...
• error in bowtie2 alignment
  hey friends, for months im working with bowtie2 but today i am getting error my reference genom...
• Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1
  I'm trying to run bowtie2. These are the commands: UNMAP=/pathtofile/unmappedreads.txt ...
• to run bowtie on multiple fastq file
  Hello all Currently i am running bowtie to align my 4 pairend reads to reference genome . I am r...
• Error while building index for ecoli referenc genome
  i am new the area of bioinformatics . Right now working on the tuxedo protocol . Trying to analyz...
• Bowtie2 index file problem in RNA-Seq mapping
  Hello colleagues, I have `.fastq` files obtained by RNA-Seq and I'm trying to map them into cus...
• Tophat error: Bowtie not found on this system
  I am trying to align RNA-seq reads to my reference but I keep getting the error: > [2016-06-0...
• Bowtie2 simple alignment errors?
  I'm new to Bowtie2 and have been trying to run some simple alignments in Bowtie2. My current bash...
• error in bowtie 2
  Dear all When I use bowtie 2 i get this error What can I do ? (ERR): bowtie2-align exited wit...
• Could not locate a bowtie index corresponding to basename -- tried previously posted solutions
  Hi, I am running on Ubuntu 16 and am trying to analyze my data with Bowtie2. I have managed to g...
• problem converting indexed fasta file to SAM format using bowtie2
  Hi, 1)I downloaded asi_ref_ASM45574v1_chrMT.fa file from NCBI. 2)I created reads using wgsim usi...
• problem with tRNAseq alignment
  I am trying to align tRNAseq data to the tRNA transcriptom. I made the index files using bowtie a...
• Indexing a reference genome
  I am Mac user trying to run Bowtie on the example data provided in bowtie manual. When I am tryin...
• Bowtie2 cannot find references
  Hi All, I am trying to align my paired-end ChIP seq data to the Arabidopsis genome (TAIR10), but...
• Bowtie2 Warnings after make command and errors after trying to use bowtie2-build
  I've been trying to run bowtie2 with no success. At first, I tried to run `make` in the bowtie2 ...
• Problems running ViromeScan - could not locate a Bowtie2 index
  Hi all, I'm trying to run ViromeScan, and used the following: $ module use /fs/project/PAS1...
• Bowtie 2: bowtie build does not create .rev index files
  I am trying to run bowtie-build in Bowtie2 in order to create the index files for mapping and eve...
• Mapping of paired end chipseq reads with Bowtie2 gives error
  Hi All I am trying to map paired end data with Bowtie 2, it shows Error, fewer reads in file sp...
• Tophat2 Bowtie2 inchoerent results?
  I am trying to align paired-end data from Illumina (300bp x 2) to a draft genome. First of all I ...
• Bowtie2 offrate option?
  I've been having a lot of problems using bowtie in conjunction with eXpress (http://bio.math.berk...
• Please help me, 'error encountered internal bowtie 2 exception (#1)'
  Hi, everyone. I have some problem.. :( /usr/bin/bowtie2-align-s --wrapper basic-0 -x chr8.fa -...
• bowtie 2 - source code requirement
  here is the part of the bowtie wrapper script , i need to get accession for the source code of fo...
• Chip-Seq analysis in Biostar handbook
  Hi All, I am trying to follow chip-seq analysis pipeline from biostar handbook. I am trying to f...