Hi everyone,
I aligned my paired-end sequencing data using Bowtie2 and processed the resulting BAM files with Picard MarkDuplicates. However,...
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Why Is My Uniquely Mapped Read Count in Samtools Higher Than in Bowtie2?
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Indexing -bowtie2, aligning - STAR and FATAL ERROR
Ciao,
I'm a Bioinformatics newbie encountering an issue with STAR alignment. I downloaded the mm10 genome and indexed it with Bowtie 2. When... -
Bowtie2 mode for Host decontamination of metagenomic samples using proxy species
Hi,
We are profiling the taxonomy of microbial communities on boreal mosses. These mosses' genome have never been sequenced. We are using Kneaddata... -
Metagenomic read classifier
Hello,
I will be doing metagenomic sequencing on clinical samples with >99% expected human reads and few microbial reads, with the microbial... -
mapping multiple low cov genomes to one ref genome
We are starting a project to explore admixture between populations of two species. We have over 40 low coverage genomes (1-5x coverage) (lcg) and a very... -
Multiple fastq alignment with bowtie2 in server
Hi!
I'm trying to map multiple sra files (>6500) with bowtie2 against my reference genome. I am running slurm script in a server. While mapping... -
Very low TopHat aligment using public available dataset
Probably I'm missing something very simple, but I'm quiet new on this and maybe you can help me to sort this out.
I've downloaded a raw... -
BS-seeker2 alignment error (bowtie2)
Hi everyone
,
I'm trying to align some of ours RRBS data on human genome hg38 with BS-seeker2.
Indexing went good without any... -
Bowtie2 exact match and same length
Hi,
I have 8 fastq files with small RNA sequencing data and I would like to allign the sequences to a reference (.fa), thereby removing the...Last edited by Aquilifer; 04-09-2018, 06:19 AM. -
Could not locate a bowtie index corresponding to basename -- tried posted solutions
Hi,
I am running on Ubuntu 16 and am trying to analyze my data with Bowtie2. I have managed to get this exact script to work on a windows... -
RNA-seq read alignment best practices for low-input Smart-seq2 samples
RNA-seq read alignment best practices for low-input Smart-seq2 samples
Hi All,
I think my data may fall in a nether region between... -
Bowtie2: a specific use where the parameters are not respected
Hello everyone,
I'm writing this post because I observed a strange behavior with bowtie2. And I suspect this behavior to affect mostly alignments... -
Bowtie2 paired end alignments do not match
Hi all,
Maybe someone already encoutered this issue... I am trying to use bowtie2 to map some paired-end reads against a set of assembled... -
Bowtie2 for miRNA-Seq
Hopefully someone can help. I have read conflicting info about aligners for miRNA data but I have finally decided on Bowtie2. I have 3 questions:
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