15
votes
What is the difference between samtools, bamtools, picard, sambamba and biobambam?
The obvious answer is that different people wrote them. It's fairly common in bioinformatics for people with a computer science background to get frustrated with existing tools and create their own ...
- 11.7k
15
votes
Accepted
Better aligner than bowtie2?
Bowtie2 is no longer the fastest aligner. Salmon and Kallisto are much faster, but have been designed to optimise RNASeq mapping. Their speed is gained from avoiding a strict base-to-base alignment, ...
- 11.7k
14
votes
Accepted
Merge hundreds of small BAM files into a single BAM file
samtools merge merged.bam *.bam is efficient enough since the input files are sorted. You can get a bit faster with sambamba and/or biobambam, but they're not ...
- 19.2k
14
votes
Accepted
Meaning of BWA-MEM MAPQ scores
First of all, if you want to understand mapping quality (mapQ), ignore RNA-seq mappers. They often produce misleading mapQ because mapQ is not important to RNA-seq anyway.
Strictly speaking, you have ...
- 5,735
13
votes
Accepted
Obtaining uniquely mapped reads from BWA mem alignment
To exclude all possible multi-mapped reads from a BWA-mapped BAM file, it looks like you need to use grep on the uncompressed SAM fields:
...
- 11.7k
12
votes
Difference between BWA-backtrack and BWA-MEM
TL;DR:
BWA-backtrack is based on backtracking.
This approach is appropriate only when the dissimilarity between the reads and the reference is low,
or when you want to find all best hits or enumerate ...
- 1,869
12
votes
Accepted
Definition of "seed" in sequence alignment
The seed is the subset of a read used in the first step of an alignment. Many aligners work by a seed-and-extend model, wherein they first find all regions matching the "seed" and then extend the ...
- 19.2k
11
votes
Accepted
Library for computing BWT-based alignments
First, let us remark that there exist several hundred read mappers, most of which have been even published (see, e.g., pages 25-29 of this thesis). Developing a new mapper probably makes sense only as ...
- 1,869
9
votes
Accepted
Aligning many long sequences
Whole genome aliment can be done using Progressive Mauve, LAST or Mummer. For bacteria I used Mauve since it has also very nice visualisation engine. A very new tool is Minimap2, a super fast mapper ...
- 5,287
9
votes
Library for computing BWT-based alignments
BWA-MEM can be used as a library. File bwa/example.c shows the basic functionality for single-end mapping. It should give identical mapping to the bwa-mem command line. Header bwa/bwamem.h contains ...
- 5,735
9
votes
Difference between BWA-backtrack and BWA-MEM
To quote the Introduction to BWA on sourceforge:
BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the ...
- 573
9
votes
Accepted
How to count the number of mapped read in 100-bp window from a BAM/SAM file
one-liner
Here's a gritty one-liner to count the number of reads in a region if you have just one region that you want to investigate. Change the 1 in ...
- 3,071
8
votes
Merge hundreds of small BAM files into a single BAM file
Merging sorted files is a linear operation, so any well-implemented tools that do it will do it with approximately the same efficiency. So samtools merge (use the ...
- 914
8
votes
Accepted
Building STAR Genome Index for nanopore RNA sequencing
The parameter is used to determine how much sequence STAR indexes on each side of a splice junction to improve its alignment accuracy. For very long reads, this may not be ideal. I am not sure if ...
- 727
8
votes
Accepted
Total reads aligning to each reference within a bam file
The quick way to get the number of alignments on each reference is
samtools idxstats my_bam.bam
Number of reads on each reference is column 3. Although, as has ...
- 3,211
8
votes
How to get fasta alignment file from SAM/BAM file?
I am not sure what you mean by "fasta alignment file". If you mean a multi-sequence alignment (MSA) in the fasta format, you can't get that because SAM keeps pairwise alignments only and doesn't align ...
- 5,735
7
votes
Accepted
Y Chromosome Aligned Reads in scATAC-seq data from a female-derived cell line?
There are homologous regions between X an Y chromosomes: https://en.wikipedia.org/wiki/Pseudoautosomal_region
It is therefore normal to have some female-derived reads mapping in Y chromosome.
You ...
- 2,960
7
votes
The effects of incomplete bisulfite conversion upon mapping efficiency
Bisulfite conversion efficiency has no effect on the mapping rate in bismark and similar tools. The reason is that the reads are fully bisulfite converted in silico before alignment to minimize ...
- 19.2k
7
votes
Accepted
What is local realignment and what is the problem it solves?
SNPs are likely to be created and InDels are likely to be missed. Suppose you have a read, ACTGACTGACTGTAC and you align it to a reference sequence ...
- 19.2k
7
votes
why in RNA seq don't we only use reference transcriptome?
Pseudoaligmnent to a reference transcriptome with something like Kallisto is perfectly valid, assuming you are in an organism whose reference transcriptome is very well documented.
But if you want to ...
- 1,662
6
votes
Accepted
Compare alignment quality of multiple sequencing runs aligned against the same reference genome
Qualimap will do this for you.
Go to qualimap.bioinfo.cipf.es
Run qualimap (default params are fine) on each BAM file
Open up the HTML output, and you can read off the %identity (they measure the ...
- 952
6
votes
Accepted
tools to reconcile experimental transcripts with reference annotation
I've never tried this myself, so I don't know how easy this is...
One option would be to start with GMAP, which is meant to align whole transcripts against the genome. The really nice thing about ...
- 19.2k
6
votes
Interpreting Intergrative Genomic Viewer (IGV)
You've apparently colored your alignments by read strand. In this case, red indicates "+ (watson) strand" and blue indicates "- (strand) strand". This strand association is determined by the ...
- 19.2k
6
votes
Accepted
Does the DNA or RNA of some ethnic groups map better than others' to the human reference genome sequence?
For simple variants like SNPs it would not really be a problem to use the current genome assembly for other ethnic groups. But for more complex variants this could be indeed problematic, however not ...
- 3,541
6
votes
Accepted
Is there a standard definition for "assembly polishing"?
In long-read assembly, "polish" refers to the step to improve the base accuracy of contig sequences. I believe the terminology was originated from the HGAP paper:
The final consensus–calling ...
- 5,735
6
votes
Accepted
Sequence alignment using Markov Model
If I understand your question correctly, then I think for case of pairwise alignment, there is a simple explanation.
I believe the key insight is that: a mismatch should always score better than a ...
- 3,462
6
votes
Accepted
How to align output of grep --color=always? (To QC fasta/fastq files)
Perhaps, grep is not the best tool to use in this case, but it should be in principle possible by using grep & ...
- 2,695
6
votes
Accepted
Can blat use more than one core/CPU to speed up the alignment?
BLAT can only use one CPU. It is actually not the right tool for full-genome alignment. For "two versions" of the same species, MUMmer and minimap2 are orders of magnitude faster and probably give ...
- 5,735
6
votes
Definition of "seed" in sequence alignment
Devon's answer gives a good, concise definition. But it's also helpful to consider why seed-and-extend is used and what benefits it provides.
Finding approximate string matches requires operations ...
- 4,938
6
votes
Frequency of specific viral sequence in .BAM or .fastq
Most read aligners will report unaligned reads as well, which presumably will include your viral sequences. I would ask them to formally confirm that the BAM files will contain unaligned reads before ...
- 4,938
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