18 results in 0.0027 seconds.
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How to get better alignment results of PAcBio data?
HI. I am trying to align PAcBio data (data from third generation sequencer) using bwa mem. I am getting very less number of aligned reads in SAM file... -
Lost pairing info after bwa mem
Dear all,
Seems I'm missing something trivial, but cant figure out.
I've got exome seq pipeline. 2 fastq files with corresponding...Last edited by ArtemLada; 01-10-2016, 01:51 AM. -
trouble with bwakit - where are the options?
Hi all,
I'm wondering if anyone has some experience with bwakit v0.7.12 and can chime in.
The command run-bwamem within... -
Quality trimming with bwa-mem
Hi,
When using bwa-mem, is it necessary to use a different program for quality trimming prior to alignment? Since FASTX toolkit doesn't work with... -
bwa mem does not output unmapped reads
Hi,
I started recently using bwa mem. Using samtools flagstat on the alignment, I see that the total reads are less than the reads in the... -
nothing aligned using bwa mem
Hi there.
I am using bwa to align human RNA-seq reads to rRNA database to exclude rRNA pollution. I tried both bwa backtrack and mem, and very... -
BWA MEM - which reads were mapped by mate-pair rescue?
Is there a way to tell which reads were mapped by mate rescue?
I learned that in BWA results there should be a XT:A:M tag in that case, but in... -
bwa mem and pindel
Dear all,
Thank you very much to all of you in advance for all the help I am sure I will receive. I am having problems running Pindel on bam files... -
Some chromosomes missing in bwa-output
Hello!
I have fasta-files, resulting from a de novo assembly. When I map pe-reads to these fastas with bwa-mem (default options), it does... -
bwa mem - failure to execute
Hello all,
I am VERY new to both working in Linux and manually performing alignments. I work in a lab that has always used Miseq Reporter,... -
Bwa mem is exiting with segmentation fault for large contigs (> 0.4Mbp)
Hello all,
I am using bwa mem to align contigs to a reference genome and I observed that it is exiting with an error message "Segmentation... -
bwa mem for compressed fastq files
Hi Everyone,
I want to use bwa mem to align my fastq files to the ref genome.
My fastq files are .bz2 compressed. Something like... -
How does BWA MEM handle reads shorter than 70bp?
Yet another quality trimming question... I've got some Illumina paired-end DNAseq data from tumor and normal samples (100bp reads). I want to align the... -
bwa-mem -C option problem with barcode field in SAM file
I recently started working bwa-mem on a 2X100 PE RNAseq dataset (ILMN cassava 1.8+) and ran into some problems with the sam/bam headers, as well as the... -
BWA MEM mapping to divergent reference
Hi,
I would like to use BWA MEM to map reads from a species without a reference genome to the closest available reference (about 3-4% diverged)....
