Questions tagged [bowtie2]

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Is the Bowtie2 MAPQ score dependent on the database index?

I have two very similar genomes in my bowtie2 database (nuc similarity > 90 %). When mapping with bowtie2 against this database, most of the reads that are mapped to one of these genomes have a ...
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1 vote
1 answer
45 views

Bowtie2 mapping with multiple indexes

Background: We performed NGS using cells collected from mice in a xenotransplantation study. As such, the FASTQ files contain reads of DNA from both mice and human cells. I expect ~30% of reads are ...
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3 votes
0 answers
17 views

GRanges coverage error with discordant reads

I mapped my fastq files from 4SU-seq experiment to human genome hg19 with bowtie 2 and got this results: ...
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1 vote
0 answers
43 views

Bowtie2 gets stuck on alignment

I am aligning a fastq file as follows: ...
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1 vote
0 answers
35 views

How to quantifiy of specific genes from shotgun metagenome?

I have googled a "lot", couldn't find any specific answer to the question. So, I am here seeking for your guidance. My question is similar to this. I have several metagenome (n=30). But for ...
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1 vote
1 answer
49 views

How to export summary data from Bowtie2 for MultiQC to read?

BowTie2 puts out summary info to the terminal but doesn't allow me to save each to a separate file. How can I go about saving the output of BowTie2 so that MultiQC can read it and create a website ...
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  • 31
1 vote
0 answers
88 views

Conversion of SAM to BAM files

I am very new to micro RNA analysis. I have been using H. sapiens, GRCh38 + major index as given in the Bowtie Website to align with my trimmed FASTQ file . The command I am using to make very ...
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1 vote
0 answers
65 views

using Bowtie to map miRNA-seq data to rfam and also reference genome

I am using Bowtie to remove non-coding RNAs (tRNA, snRNA, rRNA) by rfam and also maping our microRNA-seq data with mirbase using following code: ...
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1 vote
1 answer
66 views

fastq file format unknown

I have paired-end fastq files some of which seem to be in a weird format (from a collaborator, not a public database). When I cat the file I get what seem to me to ...
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0 votes
1 answer
124 views

How to perform bowtie2 analysis with slurm?

I am trying to run my alignment script that works locally, using SBATCH. Official manual for bowtie2 says I can use ...
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1 vote
1 answer
372 views

How can I extract information from .sam files?

I have 10 .sam files after my bowtie2 alignment on ten single-pair sequences. I would like to build a graph based on that output ...
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0 votes
1 answer
40 views

What is the best way to map/align my reads on a given genome?

I am frequently using a ballgown package for my rnaseq analysis, but recently I have had a new task to have my reads mapped on two different genomes to understand the level of alignment between the ...
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2 votes
2 answers
209 views

Filtering out reads from a reference (e.g. rRNA) using bowtie2

As I understand it, bowtie2 can easily be used to split reads into one of two groups: reads for which both of a pair align well to a reference (using e.g. ...
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0 votes
1 answer
152 views

install bowtie2 from sources cannot find -ltbb

I am trying to install bowtie2 aligner from sources without the root access. Bowtie2 needs tbb package to be installed and it is recommended to install oneTBB. ...
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  • 93
2 votes
1 answer
346 views

How to extract unmatched reads using bwa and samtools?

I have a single read (NOT paired) that I need to pass through the workflow described in Beauclair et al. paper (free version here https://rnajournal.cshlp.org/content/24/10/1285.long) for identifying ...
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1 vote
1 answer
199 views

No MQ tags in VCF files

To call minority variants in my Mtb sequences I'm using a pipeline of ...
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  • 140
1 vote
3 answers
78 views

Is BWT based aligner suitable for any types of alignment task?

Burrows wheeler transformation based aligner like BWA or bowtie seems a standard alignment tool used many area. I was just wondering if there is a kind of alignment task in which BWT algorithm is not ...
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  • 11
2 votes
1 answer
190 views

Read alignment using Bowtie2

So this is related to CRISPR-CAS9. I am working with off-target predictions for my thesis and was looking at all scientific papers related to CRISPR. I found one and decided to use their datasets. The ...
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  • 21
4 votes
1 answer
552 views

How to get a MSA fasta from BAM/SAM?

I am working with paired end NGS miseq data from a viral genome with multiple timepoints. I have filtered and trimmed this data for quality and adapter sequences. I have then merged the filtered ...
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  • 41
0 votes
1 answer
1k views

bowtie2 options when mapping stranded single end reads

I'm trying to map RNA-Seq reads generated using the NEB Ultra Directional kit is first strand reversed protocal. I'm using bowtie-2.3.5_1 to align against the mus ...
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3 votes
3 answers
310 views

Alignment with arbitrary number of mismatches or gaps

I have 23bp long reads and want to find all possible alignments of them to the human genome (hg19, hg38) for an arbitrary number of mismatches (<7), possibly also small indels. I've read in ...
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3 votes
1 answer
255 views

Seeking explanation of the hg38 files downloaded from bowtie 2 website

I downloaded the H. sapiens, NCBI GRCh38 files from Bowtie's website. After unzipping, there are 6 files, 4 that end in set 1.ebwt, set2.ebwt, set3.ebwt, and set4.ebwt and two that end in set.rev.1....
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