Questions tagged [bowtie2]
The bowtie2 tag has no usage guidance.
25
questions
3
votes
2
answers
93
views
Cannot obtain alignment summary after running Bowtie2
I am aligning my Small RNA Seq data with Bowtie 2. Although the alignment performs well, the only information I obtain after finishing running the alignment is the following:
...
4
votes
1
answer
204
views
Breseq error (code 137). Any ideas?
The code I ran was here, so nothing fancy.
breseq -l 110 -o RifR_align -r Big_burk_assembly.fasta RifRNano_nanopore.fastq.gz
This was the output.
...
3
votes
2
answers
2k
views
STAR vs Bowtie2
What is the fundamental difference between STAR and Bowtie(2). Specifically, what is the difference in their final output (regardless of run-time differences, speed, memory usage etc.). Both seem to ...
- 323
2
votes
2
answers
112
views
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 ...
- 23
1
vote
1
answer
440
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 ...
- 237
3
votes
0
answers
26
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:
...
- 51
2
votes
0
answers
81
views
1
vote
1
answer
76
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 ...
- 111
0
votes
1
answer
240
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 ...
- 21
1
vote
0
answers
776
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 ...
- 143
1
vote
0
answers
184
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:
...
- 11
1
vote
1
answer
186
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 ...
- 11
0
votes
1
answer
300
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 ...
1
vote
1
answer
1k
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 ...
0
votes
1
answer
42
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 ...
2
votes
2
answers
674
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. ...
0
votes
1
answer
256
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.
...
- 203
2
votes
1
answer
1k
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 ...
1
vote
1
answer
391
views
No MQ tags in VCF files
To call minority variants in my Mtb sequences I'm using a pipeline of
...
- 152
1
vote
3
answers
106
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 ...
- 11
2
votes
1
answer
278
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 ...
- 21
4
votes
1
answer
836
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 ...
- 41
0
votes
1
answer
2k
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 ...
5
votes
3
answers
580
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 ...
- 105
3
votes
1
answer
380
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....
- 31