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 ...
- 13k
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.
...
- 6,295
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.
...
- 176
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 ...
- 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 ...
- 6,295
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 ...
- 5,467
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.
- 827
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 ...
- 755
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 ...
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 ...
- 353
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 ...
- 105
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 ...
- 108
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.
...
- 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
- 352
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 ...
- 737
1
vote
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
...
- 11
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.
- 1,812
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