User: lanyuhao1991

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lanyuhao199110
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China
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4 years, 5 months ago
Joined:
6 years, 4 months ago
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Posts by lanyuhao1991

<prev • 9 results • page 1 of 1 • next >
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Discovar assembly with big data with lack of memory size?
... https://groups.google.com/a/broadinstitute.org/forum/#!topic/discovar-user-forum/1sagrgk7suE ...
assembly written 4.5 years ago by lanyuhao199110
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Answer: A: Discovar assembly no reference reads(urgent)
... There are more information in [google group](https://groups.google.com/a/broadinstitute.org/d/msg/discovar-user-forum/YcUAxG80-lw/6lo_eKHSAwAJ) ...
written 4.6 years ago by lanyuhao199110 • updated 6 months ago by RamRS27k
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Discovar assembly no reference reads(urgent)
... Hi all, I need your help. I have reads(fastq,pair-end) that have no reference genome. I want to use Discovar to assembly(no reference). I use the following step: 1. First, I convert pair-end fastq files to bam file. (for example, a1.fastq, a2.fastq->a.bam) The bam has no region information beca ...
assembly no reference reads discovar written 4.6 years ago by lanyuhao199110
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How can I get the informaiton about base quality(BQ) in VCF file?
... Hi everyone, I use samtools(version 0.18) to do snp calling.But the final VCF(version 4.1) file do not have the BQ(base quality). How can I get the informaiton about BQ ? Because I should filter the VCF files based on BQ > 15. The command : samtools mpileup -uf ref.fa aln.bam | bcftools vie ...
vcf bq snp written 6.1 years ago by lanyuhao199110 • updated 6.1 years ago by Dan D7.1k
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Comment: C: Two Ways To Get Coverage Of Bam But Why Do The Result Is Different?
... 0x4 segment unmapped;0x8 next segment in the template unmapped; I think use -F 4 or -F 8 in pair-end map will get the same result. This is not the key to my question. Thank you for your reply. ...
written 6.2 years ago by lanyuhao199110
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Comment: C: Two Ways To Get Coverage Of Bam But Why Do The Result Is Different?
... Use -F 8 to filter ummaped mates can have the same result as use -F 4.I do the test, the result is same. But use -F 12 can filter the pair-end reads including that only a mate is unmapped. http://samtools.github.io/hts-specs/SAMv1.pdf ...
written 6.2 years ago by lanyuhao199110
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Two Ways To Get Coverage Of Bam But Why Do The Result Is Different?
... Hi, I use MosaikAligner to map pair-end reads to the genome(know the genome_size). I get the bam format file(a.bam). a.bam have all the mapped results including the unmapped,the mapped (unique-anlignmed and multiply-aligned) reads. I want to get the coverage and coverage rate of a.bam. I use 2 ways ...
samtools coverage written 6.2 years ago by lanyuhao199110
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Count The Coverage Rate Of A Bacterial Genome'S Bam File
... I have the bam file. I want to count the coverage rate of a bacterial genome. For example, the size of a bacterial genome is 10000 bp. Reads have been mapped to the genome. I use 'samtool depth' and I get 6000 Nucleotide site have been coveraged. So the coverage rate is 60%. But I find some same rea ...
genome bam coverage map written 6.2 years ago by lanyuhao199110 • updated 6.2 years ago by Fidel1.9k
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What Can We Do For The Reads That Are Not Mapped To The Genome?
... I have the reads of the some mammals intestinal microflora. I mapped the reads to the bacteria genomes. And I want to use the rest of reads that are not mapped to do something. I want build some new genomes of bacterium. Can you give me some advice for: 1.how to build some new genomes of bacteriu ...
reads map written 6.2 years ago by lanyuhao199110 • updated 6.2 years ago by Haluk170

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