Hi,
I have a bam file that includes a big indel and a translocation. I wish to extract a new reference fasta file with the SV (without the deleted...
10 results in 0.0022 seconds.
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extract fast from bam taking SV into account
Last edited by EHC; 03-16-2022, 01:10 AM. -
incredible high memory consumption of bwa-mem on small amplicon dataset
Hi all, I am working with Human amplicon data and have been using bwa mem (0.7.15) up to now. Unfortunately, on some datasets the memory consumption exceeds... -
Selecting the best alignment BAM file
Hi,
I have a PE dataset 300bp inserts by illumina MiSeq. I aligned the raw data using BWA-mem. Mapping statistics generated using Samtools... -
SOAPindel with bwa-mem
Has anyone run SOAPindel on sequences aligned with bwa-mem? It seems to have trouble interpreting some of the lines of the bam. -
STAR Aligner
I am running STAR for aligning wheat RNA-Seq data with Ensemble reference file . The size of reference file is 4gb. The genome directory created in the... -
High Percentage of Soft Clipping, BWA-MEM, MiSeq
Hi everyone,
I have 1,377,239 paired reads, 250bp each, 82,486 of them have been soft clipped for more than 200bp (eg a read with CIGAR... -
Mapping multiple FASTQ data types using BWA?
Greetings!
I plan to do mapping using multiple types of Illumina FASTQ files for the same sample.
I have one set of FASTQs... -
Secondary Alignments with BWA-MEM
When I have split reads originating from repetitive sequences I must use the -a flag to get the secondary alignments. The problem with this is that with... -
how many mismatches does BWA-MEM tolerate during mapping
Hi,
Recently I am trying to use BWA-MEM to do alignment on PE-90 reads, I have some questiones list as following;
1,how... -
BWA automatic parameter estimation
Hi,
I am using Illumina paired-end data (read length 250 bp) for producing a bam file using BWA and Samtools. As BWA does not support...
