Skip to main content
6 votes
Accepted

Alignment with arbitrary number of mismatches or gaps

This is not something mappers will be good at, because you're going to hit most of the genome. Bowtie won't do it, and I don't think LAST will either. The majority of fast mapping programs rely on ...
gringer's user avatar
  • 14.4k
6 votes

STAR vs Bowtie2

What is the fundamental difference between STAR and Bowtie(2). STAR for mapping spliced (i.e. with introns) short RNA-seq reads against a genome. Bowtie2 for mapping short reads without splicing. ...
user172818's user avatar
  • 6,545
5 votes

Cannot obtain alignment summary after running Bowtie2

Remove the --quiet option, and capture STDERR as well as STDOUT: ...
Timur Shtatland's user avatar
3 votes

STAR vs Bowtie2

The seeds are clustered together by proximity to a selected set of ‘anchor’ seeds in the 2nd phase of the STAR algorithm, but this •clustering/stitching/scoring process• is not present in Bowtie2. ...
envs_h_gang_5's user avatar
3 votes

fastq file format unknown

This indeed looks like some sort of binary file. I have seen bunch of those when people renamed .fastq.gz to .fastq without ...
Kamil S Jaron's user avatar
3 votes
Accepted

How to perform bowtie2 analysis with slurm?

It seems you do not have bowtie installed or loaded. Use module load bowtie2 together when you load samtools.
Phoenix Mu's user avatar
3 votes

Seeking explanation of the hg38 files downloaded from bowtie 2 website

Bowtie is providing you with the index files for hg38. This are the result of the bowtie2-build indexer. However you have downloaded the indexes for Bowtie1 not bowtie2 Bowtie 2’s .bt2 index ...
Bioathlete's user avatar
  • 2,574
3 votes

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

BWT based algorithm is just a component of a full-pledge aligner. To that end, it is applicable to most alignment tasks. However, for long-read alignment and metagenomes, we don't often use BWT based ...
user172818's user avatar
  • 6,545
3 votes
Accepted

Aligning FASTQs to FASTA reference

Can I expect that after running the command bowtie2 -x ref_index -U seq.fastq.gz -S seq.sam, my seq.sam will only contain the ...
terdon's user avatar
  • 10.2k
2 votes

Alignment with arbitrary number of mismatches or gaps

I've ended up using a package called BatMis for this, which can detect alignments with an arbitrary number of mismatches (not sure about indels). It is quite performant and yields about the order of ...
Flagon13's user avatar
  • 105
2 votes

How to get a MSA fasta from BAM/SAM?

If need to get msa between every read and ref in the specific region , you can try this https://github.com/orangeSi/bam2msa.git ...
orange's user avatar
  • 21
2 votes
Accepted

How can I extract information from .sam files?

Use samtools flagstat with option -O tsv: Using -O tsv selects a tab-separated values format that can easily be imported into ...
Timur Shtatland's user avatar
2 votes

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

If you want to remove rRNA, use tools that are made for this. We usually go for SortMeRNA, which can do exactly what you describe your goal is, i.e. go from FASTQ to FASTQ, splitting your reads into ...
Bastian Schiffthaler's user avatar
2 votes
Accepted

No MQ tags in VCF files

As @ATpoint explains in his comment, the mapping quality (MQ) applies to read mappings and, hence, is contained in BAM files, but not VCFs. The ...
mrhd's user avatar
  • 363
2 votes

Cannot obtain alignment summary after running Bowtie2

Get samtools. Then run: samtools stats file.bam and/or samtools flagstat file.bam For example outputs see here.
Maximilian Press's user avatar
1 vote

Breseq error (code 137). Any ideas?

[Not quite an answer but too long for a comment] I am guessing that your assembly Big_burk_assembly.fasta is a rather large assembly. Assembly indexing can be very ...
Maximilian Press's user avatar
1 vote

How to quantifiy of specific genes from shotgun metagenome?

The way I would do it is to make an assumption that the reads mapping to your contig == (abundance of the genes in the contig)/contig length. Map raw reads to the contig containing your hit (original ...
Avamys's user avatar
  • 118
1 vote

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

After trying on my own this is the solution I came up with. My solution was to use a pipe of the stderr into a new file. ...
Stephan's user avatar
  • 21
1 vote

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

Not sure about the algorithm itself but Heng Li wrote an article about the future of BWA when releasing minimap2. It gives helpful insights about the topic : Heng Li's blog
Paul Endymion's user avatar
1 vote

install bowtie2 from sources cannot find -ltbb

You need to give the path to the source files for the compiler and the full path to the compiled libraries (all parent directories included) for the linker. You also need to use either CPATH or ...
Jesse's user avatar
  • 947
1 vote

bowtie2 options when mapping stranded single end reads

I repeat what user172818 says...don't waste your time on bowtie or tophat. Use STAR or HISAT2, or a pseudoaligner like kallisto with a transcriptome.
swbarnes2's user avatar
  • 1,941

Only top scored, non community-wiki answers of a minimum length are eligible