User: lghust2011

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lghust201190
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Posts by lghust2011

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Comment: C: How can I restore paired-end fastq files from a sorted bam file with fastq remai
... Thanks for your answer! ...
written 2.0 years ago by lghust201190
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Comment: C: How can I restore paired-end fastq files from a sorted bam file with fastq remai
... I want to get the sorted fastq files, so I can get the sorted sam file directly when I run BWA MEM with sorted fastq files. But it seems very difficult! ...
written 2.0 years ago by lghust201190
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Comment: C: How can I restore paired-end fastq files from a sorted bam file with fastq remai
... Either sam or bam format is OK for me ...
written 2.0 years ago by lghust201190
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How can I restore paired-end fastq files from a sorted bam file with fastq remain sorted?
... I have two paired-end FASQ files named fq1.fastq and fq2.fastq. Then I use BWA MEM to map these two files with the paired-end mode, like this: bwa mem reference.fasta fq1.fastq fq2.fastq > result.sam Then I transfer this sam file to bam format and sort it by coordinates with samtools: ...
alignment sequence written 2.0 years ago by lghust201190 • updated 2.0 years ago by Carlo Yague4.8k
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Mutect2 gets different results when I change the downsample level
... I use mutect2 of GATK 3.6 and GATK 3.7 to call variant. I know there is a downsampling in mutect2 which has an important influence on the result. So I change the downsampling level. For example: the default value is: maxReadsInRegionPerSample = 1000; minReadsPerAlignmentStart = 5; I change ...
gene alignment next-gen sequencing written 2.5 years ago by lghust201190 • updated 2.5 years ago by Dan Gaston7.1k
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Comment: C: BWA: Why paired reads mapped to different chromosome?
... I got fq1.fastq and fq2.fastq from the sequencer directly. By default BWA will get read1 from fq1.fastq and get read2 at the same order from fq2.fastq. Is it possible that these two reads are not exactly from the same DNA fragment? Why? ...
written 2.6 years ago by lghust201190
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Comment: C: BWA: Why paired reads mapped to different chromosome?
... Do you mean the **read1** from fq1.fastq and **read2** from fq2.fastq are not from a same DNA fragment? ...
written 2.6 years ago by lghust201190
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Comment: C: BWA: Why paired reads mapped to different chromosome?
... Yes, it's a cancer sample. If it's a normal sample, paired-reads will mapped to different chromosome? I think repeat sequence is frequent.. ...
written 2.6 years ago by lghust201190
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Comment: C: BWA: Why paired reads mapped to different chromosome?
... The sample is from a patient and my reference is hs37d5.fa. Around 2% of paired-reads are mapped to different chromosome, however, most of their MAPQ is 0. So, may I remove these paired-reads? Will they influence the vcf result? My pipeline is bwa->samtools->picard->localrealign->BQSR-&g ...
written 2.6 years ago by lghust201190
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BWA: Why paired reads mapped to different chromosome?
... I use BWA-MEM to map reads to reference, the command line is below: ``` bwa mem -t 6 reference.fasta fq1.fastq fq2.fastq > result.sam ``` According to the source code, BWA will get read1 from the fq1.fastq, and get read1 from the fq2.fastq. By default, read1 and read2 are paired-end reads from ...
genome alignment sequencing written 2.6 years ago by lghust201190

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Student 2.6 years ago, asked a question with at least 3 up-votes. For BWA-MEM get different results with different threads

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