I have received a project and could use some advice.
My task is to find sequence matches in mRNA databases across 20+ taxa. I was presented...
303 results in 0.0045 seconds.
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Finding transcriptome matches for thousands of 21-mers
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Insertions follow reference in vcf file
Hi,
I'm working with gvcf files, containing also non-variant positions. I have noticed some insertions that I'm not able to correctly interpret... -
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Quality Control, Read Mapping, Visualization and DNA Variant Analysis
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Surprising Alignment
Hi,
I have been working with some WES files and getting surprising results, in which very rare variants are being found much more often than... -
Which parameter is reflecting the maximum number of mismatches when using bwa aln
I have seen some discussions about this but still cannot confirm the answer.
My question is that if I want to allow 3 mismatches when using bwa... -
mapping hundreds of RADseq fastqs to ref genome.
I would like to map hundreds of fastq.gz single-end RADseq files to a single reference genome.
But, bwa mem is making a map file (.sam)... -
Stampy software error with PairSorter
Hi all,
I am trying to map reads (Paired End) from a sample to a reference assembly that is somewhat divergenct (~3%). So I used the bam file... -
SUBJECT: Stampy software error with PairSorter
Hi all,
I am trying to map reads (Paired End) from a sample to a reference assembly that is somewhat divergenct (~3%). So I used the bam file... -
BWA SW's equivalent for MEM's "-C" option?
Please delete that thread, I should use the latest version of bwa, there is the "-C" flag for BWASW as well... -
Loop in bwa commands
Hiya,
I'm trying to loop multiple input files with matching prefixes and different file types in bwa sampe ; here's the general structure:... -
Wrong bwa alignment?
Hi,
Below is a supplementary alignment for one of my reads with a mapping quality score of 43.This should map to chr2: 29446797 in hg19
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bwa GATK4 read group issues
Hello,
I am trying to run GATK4 HaplotypeCaller on bam files from single individuals generated with bwa mem on Ubuntu 18 with
...Code:$gatk HaplotypeCaller
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mapping multiple low cov genomes to one ref genome
We are starting a project to explore admixture between populations of two species. We have over 40 low coverage genomes (1-5x coverage) (lcg) and a very... -
Failure in running BWA on human fusion genome
Dear all,
I have used the fasta genome provided by NCBI. The headers of this file are:
>chr1 AC:CM000663.2 gi:568336023...
