User: bioxujintian

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Posts by bioxujintian

<prev • 11 results • page 1 of 2 • next >
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Comment: A: QIIME - Illumina MiSeq, Paired-end Data - Mapping file and Data Preprocessing Qu
... Hi, Sara Thank you for you reply. I still confused after looked the thread. My sequencing data didn't demultiplexed, I only have paired-end reads(Read1 and Reads2, which all samples contained in this two files), and 2 barcodes, 2 index reads for each samples. How should I do to set up mapping file ...
written 17 months ago by bioxujintian0
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Comment: A: QIIME - Illumina MiSeq, Paired-end Data - Mapping file and Data Preprocessing Qu
... Hi, Sara Have you solved the problem? I have same problem with you. My sequence data is from Illumina, paired-end reads, and one sample have 2 barcodes, 2 index reads, I don't know how to set up mapping file for Qiime software. Do you have any suggestions? Thank you! Jintian ...
written 17 months ago by bioxujintian0
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How can I use rdp classifier method when use pick_open_reference_otus.py
... Hi, Everyone I am new in use Qiime software to analysis 16S-sequencing data. When I use pick_open_reference_otus.py and want to use rdp classifier method to pick otus, but the default method is uclust, I don't know how to set the parameter. Someone can help me? Thank you very much. ...
pick_open_reference_otus.py qiime written 17 months ago by bioxujintian0
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Forum: MutSigCV question: Why V1.3 and V1.4 have great different result?
... Hello, everyone I have 300+ cancer-normal matched samples, and use GATK+Mutect2+ANNOVAR to call somatic mutations and annotation, and R package maftools to transfer to MAF file. Then I use MutSigCV1.3 and MutSigCV1.4 to identify sinificance genes, but there is great different in number of genes wit ...
forum mutsigcv written 2.2 years ago by bioxujintian0
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Comment: C: How to use MutSigCV correctly
... Dear poisonAlien, I take your advice to use SpeedSeq tool to call somatic snp,but when I use speedseq somatic command,I don't konw how to create tumor or normal bam file from raw WGS samples,respectively.Can you help me?Thanks... ...
written 3.0 years ago by bioxujintian0
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Comment: C: How to use MutSigCV correctly
... Thanks a lot,I learn so much from you these days. SpeedSeq is good tool to analysis sequencing data.Maybe now I will learn SpeedSeq and MuTect first and if I have question,I will ask you, thank you very much. ...
written 3.0 years ago by bioxujintian0
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Comment: C: How to use MutSigCV correctly
... Thanks for your reply again.I have 102 vcf file,which called snp for each sample,it isn't somatic snp,but for each-sample's snp.Can I use these file for MutSigCV after using Annovar? Maybe I should do some other work? ...
written 3.0 years ago by bioxujintian0
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Comment: C: How to use MutSigCV correctly
... Thank you for your reply, poisonAlien. I had call snp for another data set(51 cancer-normal samples) use BWA and GATK for each sample.  Next step, should I use VEP to annotation?  and then, how can I concatenate these file to a vcf and should I use vcf2maf? ...
written 3.0 years ago by bioxujintian0
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Comment: C: How to use MutSigCV correctly
... I only have the fastq files, and I use Linux to work. How should I do next? ...
written 3.0 years ago by bioxujintian0
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Comment: C: How to use MutSigCV correctly
... Thank you for your answer. I'm sorry to tell you I can't visit the script to generate maf file you provided.So I have two questions: 1. How can I produce maf table from raw sequencing data(cancer-normal),should I use BWA,GATK and other software?Can you tell me the pipeline to produce the maf table ...
written 3.0 years ago by bioxujintian0 • updated 5 days ago by RamRS18k

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to use MutSigCV correctly

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