Questions tagged [bwa]
bwa (Burrows-Wheeler Aligner) is a software for aligning reads obtained with Next Generation Sequencing.
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Obtaining uniquely mapped reads from BWA mem alignment
This is based on a question from betsy.s.collins on BioStars. The original post can be found here.
Does anyone have any suggestions for other tags or filtering steps on BWA-generated BAM files that ...
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Meaning of BWA-MEM MAPQ scores
Does anyone know what the MAPQ values produced by BWA-MEM mean?
I'm looking for something similar to what Keith Bradnam ...
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Why is bwa-mem the standard algorithm when using bwa?
The industry standard for aligning short reads seems to be bwa-mem. However, in my tests I have seen that using bwa backtrack (bwa-aln + bwa-sampe + bwa-samse) performs better. It is slightly slower, ...
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How does the BWA-MEM algorithm assign its mapping qualities?
Is there any resource (paper, blogpost, Github gist, etc.) describing the BWA-MEM algorithm for assigning mapping qualities? I vaguely remember that I have somewhere seen a formula for SE reads, which ...
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Library for computing BWT-based alignments
I am writing a software tool to which I would like to add the ability to compute alignments using the efficient Burrows-Wheeler Transform (BWT) approach made popular by tools such as BWA and Bowtie. ...
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Difference between BWA-backtrack and BWA-MEM
Many of my colleagues recommend I use BWA-MEM instead of regular old BWA. The problem is I don't understand why and reading the BWA man page doesn't seem to help the matter.
What is the difference ...
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What is mate rescue in bwa mem?
BWA mem has the -S and -P tags for skip mate rescue and skip pairing; mate rescue performed unless -S also in use.
What do ...
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What are all the reference files produced by bwa index, and are these dependent upon whether the reference is zipped?
I have indexed a gzipped reference with bwa: bwa index reference.fa.gz, which produces a series of other files ...
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What is the correct way to map Hi-C data with bwa mem?
Library Prep
I have a Hi-C library prepped using an enzyme that cuts at GATC, so it leaves GATCGATC as the junction sequences. ...
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Sequence alignment using BWT
My Problem:
Skipping some specific background, what I want to do is judging whether some soft-clipping sequences are the same, which may result by the same SV event. Colored bases in Fig.1 is an ...
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Why most aligners do not output the "X" CIGAR operation?
As I read the SAM spec, the "X" CIGAR operator represents a mismatch. This seems useful as we can know where are the mismatches without looking at the reference genome. However, many popular aligners ...
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Is there a more elegant solution to the bwa-mem: paired reads have different names error?
I'm currently trying to run bwa-mem on Influenza substrains using the following command:
~/bwa mem h5n1_1_cons.fa h5n1_1_read1.fq h5n1_1_read2.fq
h5n1_1_cons.fa ...
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How to output all sequences with bwa mem, not `*`?
I've been running bwa mem -a for alignment, using the -a flag---this will
output all alignments for SE or unpaired PE
I've ...
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Do you use SNAP for short-read mapping?
I am calling SNPs from WGS samples produced at my lab. I am currently using bwa-mem for mapping Illumina reads as it is recommended by GATK best practice. However, bwa is a bit slow. I heard from my ...
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Estimating BAM file from compressed fastq file size
Is there a way to estimate the size of a BAM file will have after mapping with BWA?
The input file are two mates fastq files, compressed with gzip, each one about 70G.
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Interpreting 0x200 flag in bwa-mem alignments
I am looking at the bwamem.h code in http://github.com/lh3/bwa and found that BWA-MEM will give flag 0x200 to what it calls ...
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What is the meaning of the "*" character in bwa fastmap's output?
I am mapping kmers back to a few bacterial genomes using bwa fastmap:
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How does Li and Durbin's BWA paper compare alignment programs on real data?
Li and Durbin's "Fast and accurate short read alignment with burrows-whleeler transform" found here, says:
We evaluate the performance of BWA on ... real paired-end data by
checking the fraction ...
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BWA mem | samtools view: Intermittent parsing error
Update
The issue was that bwa was running out of memory and failing, but that error wasn't floating to the top (see @Steve's answer, below). I was getting an error ...
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Problems to Extract uniquely mapping reads from BWA MEM alignment
I did a mapping of genomic paired-end reads to a reference assembly using bwa mem. I need to extract the reads that mapped only once to my reference.
For that, I have tried to follow the method ...
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How to read .bwt file .sa file?
In BWA project in bwt.c file I found bwt_dump_bwt method and bwt_dump_sa method. I want to use them to read .bwt file and .sa file. I wrote the following program:
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How to map reads shorter than 32bp with minimap2?
I mapped fasta sequences to a reference. The fasta sequences range in length from 17bp up to several hundred bp. I used minimap2 with the following command: ...
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What can be the bias of aligning paired-reads in a single-end mode?
I don't know if I'm in the right place but I have a technical problem to fix. I would have to align paired-end reads from Illumina sequencing to compare a normal genome with a tumor one.
When I align ...
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Error with BWA Mem input having multiple fastq files using cat and process substitution
Running BWA Mem on a number of paired end fastq files using process substitution on the inputs results in this error:
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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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BWA-mem and sambamba read group line error
this question has been asked [and answered] on Stack Overflow
This is a two-part question:
help interpreting an error;
help with coding.
I'm trying to run bwa-mem ...
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How does split reads look like in sam files?
I used bwa mem to align the DNA with the reference genome. If there are split reads (chimeric reads, come from two different parts of the genome), will it be split into two lines rather than one line?
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Generating burrows-wheeler-transform and a suffix array of a DNA sequence with less memory
Also posted on biostars
After indexing
bwa index -a bwtsw reference.fa
I got files. like .bwt file and .sa file. The naive way of generating these file is:
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Minimap2 -ax map-pb doesn't output tlen field
I have used minimap2 to map some pacbio reads to a reference genome. I would like to know the "insert size" (true length of sequence) relative to the reference. More specifically, I want to know the ...
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How to take into account alternative bwa mem mapping when computing coverage
when mapping short reads with bwa mem, if a read has alternative mapping positions they are reported by bwa mem in the X0 and XA tags.
Now, let's say I want to compute the coverage of my bam file. ...
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Mark BWA-SW split alignments in output for long reads
Is there a way to remove split alignments of single-end long reads from BWA-SW output? BWA-MEM has an option to include or flag split alignments in the result, but it seems BWA-SW method include them ...
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How BWA generate index files?
I need to know how BWA generate bw and sa in less memory usage. I didn't find details in the original paper. Do they save all rotations temporary ? I need to know do BWA stores all rotations so that ...
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BWA doesn't recognize HiC options
I'm trying to run bwa on HiC data. This is the command I'm giving:
bwa mem -5SP -T0 -t4 -R '@RG\tID:\tSM:\tLB:\tPL:ILLUMINA\tPU:none' REFERENCE.fa PAIR1.fq PAIR2.fq
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Trying to create a .bam file without the need for a .sam file
I'm trying to use the code specified in this link to create a .bam file without the need for a .sam file.
Here is the code I'm using:
...
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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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Samtools Index: Chromosome Blocks not Continuous
I am working with short-read whole-genome sequences from the NCBI's SRA. I have aligned and sorted all of my short-read sequences and am attempting to index each sequence into .bai format using ...
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BWA: Detecting Variation between Reference Genome and Short-Read Sequences
I need to identify all loci in the short-read sequence at which the number of microsatellite repeats (i.e. number of copies of "AA," "GTC," etc.) differ from the reference genome, ...
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Compare mapped reads from BWA -MEM and STAR from .bam files
I want to find and compare the results from STAR and BWA- MEM mapped. I have 150bp paired end reads in sorted.bam files in each case and i want to find in each case uniquely mapped reads, number of ...
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How fo force nextflow to repeat a process until all values in a particular channels are used up BUT a single value from another channel is needed
I am trying to find a hack for getting a process to run until all emissions in a channel are used up. The problem is that the process also takes as input a second channel that only has a single ...
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Why does BWA MEM orientation contradict my library prep method
I have some RNA-seq data from a stranded paired end library prep, with dUTP and UDG preparation, so the orientation should be RF (confirmed with sequencing provider). I assembled the reads with ...
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No MQ tags in VCF files
To call minority variants in my Mtb sequences I'm using a pipeline of
...
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Slow bwa shm "preloading" into memory
Coming from devops background, working on automating usual genomics pipelines, I am benchmarking existing pipelines in order to choose cloud resources properly.
Past week most of work was on testing <...
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How can I get unmatched reads for defective genomes analysis using bwa and samtools?
I am trying to follow the Beauclair et al. paper (free version here https://rnajournal.cshlp.org/content/24/10/1285.long) for identifying defective genomes using their DI-tector program.
According to ...
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How to map multiple CDS sequences to exome data using bwa mem?
Normally, I use bwa-mem to map my fastq reads for a bunch of species using one protein-coding gene CDS from my reference species. This was fine when I had to try it for just a group of genes...I would ...
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bwt suffix array construction
I found a very good link to generate bwt suffix array in BW based tools.
@user172818 provides a nice code. could anyone tell me how to store SA elements' original position in the original string?
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Variant calling for a subset of genes using whole gneome sequencing data
I have few 100 raw fastq files from whole-genome sequencing data and I would like to map these files to a set of genes only (and not whole genome) so as to find SNP's associated with them. Can anyone ...
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samtools view: writing to standard output failed: Broken pipe
I have the following alignment script which uses BWA:
...
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Can bwameth accept unaligned Bam?
Does bwameth accept bam (unaligned) type as input or I will have to convert unaligned bam to fastq (samtools fastq bam) to use ...
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Proper use of BWA MEM on multiplexed GBS sample
I have a multiplexed lane of GBS sequencing reads as a fastq file. I understand the first step is to demultiplex and trim the adapter sequences from the reads.
This yields many individual fastq files ...
