Questions tagged [bwa]
bwa (Burrows-Wheeler Aligner) is a software for aligning reads obtained with Next Generation Sequencing.
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Running bwa mem and samtools in one script on a linux cluster
I am trying to write a script that will run this line from https://github.com/kmceres/Mbovis_pangenome/blob/main/Parameter_file.md:
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bwa mem hangs after a few thousand reads
I am trying to align a bunch of paired sample fastq files using bwa mem.
My original command was:
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low mapping percentage in bwa mem
After aligning paired-end reads to a reference genome, I am getting low percentage:
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what does 8 stands for in bwa mem command line
What does this command implies in bwa mem
bwa mem -t 8 index/referencegenome.fna read1.fastq.gz read2.fastq.gz > output.sam"""
What does ...
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Reference genome (bwa -mem)
I want to do mapping with bwa mem. I downloaded a reference genome from ncbi database which is (Danaus plexippus). I got one ncbi_database.zip file which contain 2 ...
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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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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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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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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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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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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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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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