Hi there,
I'm trying to use bwa to align Paired-end reads to mouse genome. The alignment step goes well, but the bwa samse failed and generated...
303 results in 0.0043 seconds.
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featureCounts does not recognize BWA XA tag?
Hello,
I am using featureCounts option -M. In the user guide, it says if it is specified, multi-mapping reads will be counted. The program... -
BWA -q soft clipping: Which alignment quality threshold to choose?
I wish to align to human genome samples sequenced in a Illumina HiSeq 4000. Most reads (single end) are between 20-40bp long, clean from adaptors. The...Last edited by Eurioste; 01-12-2018, 07:56 AM. -
BWA sam -> bam in pipeline
I am trying to use BWA mem to align pair-end reads to a single genome and pipe the sam file output to a bam and then a bedfile. The pipeline doesn't seem... -
Read direction lost with BWA in SAM output?
I've tried two different header styles in my input FASTQ headers when running BWA:
@SN7001163:162:C4A1UACXX:1:1101:1062:2076/1
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Tablet viewing issue
Hello everyone,
I'm new to the forum and maybe to ... bioinformatics.
I'm studying viral genome insertions into human genome.... -
A question on Illumina paired-end reads alignment. Merging from different samples
Hi folks, I have a question on how to better merge paired-end reads coming from different samples. Basically, we do align genome resequencing fastq with... -
extended cigar in bwa-mem
Hi all,
I am aligning pacbio reads to a reference genome using bwa mem. Do you know how to output an extended CIGAR in output sam file... -
Where is alignment score when using bwa aln and sampe commands are used ?
I used bwa aln and bwa sampe commands. But in the output I can't find AS tag.
It seems AS tag is reported by bwasw and is long-red specific,... -
How Do Mappers Handle Chromosome Ends?
I am trying to figure out how BW-based mappers like BWA and Bowtie handle reads that map at the end of the reference and extend off the end. One example... -
BWA mem on interlaced fastq
Hi, everybody,
I am trying to use bwa mem (v. 0.7.12) on some interleaved fastq files, i.e. the reads are paired end, but they are in one...Last edited by mstagliamonte; 04-13-2016, 06:08 AM. -
mutationalMeltdown started a topic Assigning taxonomy to shotgun metagenomic reads: sequence alignment or composition?in MetagenomicsAssigning taxonomy to shotgun metagenomic reads: sequence alignment or composition?
I'm interested in identifying bacterial pathogens from shotgun metagenomic data. Crudely, I envisage the pipeline to be something like this:
1)... -
bwa sampe on multiple samples at once
I'm looking to loop through many samples using the bwa sampe command.
Here is what the command looks like for one sample:
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Need help understanding the method from this paper
I'm trying to somehow follow the method outlined in this paper for calling breakpoints after assembly and mapping to the reference (see Assembly and Validation).... -
Duplicate read names - BWA mem - paired reads have different names
Hi,
running BWA mem (- PE; - Illumina), I'm getting the following error (replaced the ids):
[mem_sam_pe]...
