User: Yan He

gravatar for Yan He
Yan He240
Reputation:
240
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New User
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Last seen:
4 years, 3 months ago
Joined:
6 years, 5 months ago
Email:
y******@hotmail.com

Posts by Yan He

<prev • 24 results • page 1 of 3 • next >
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How To Lauch Bulit Cluster On Cloudman?
... Dear all, I just established Galaxy Cloudman on Amazon EC2. I created a cluster named "exon_capture" and uploaded a lot of data to it. After some analysis, I terminated the cluster. The second time I wanted to get access to the "exon_capture" cluster, I created a new instance under the "exon_capt ...
galaxy written 4.3 years ago by Yan He240 • updated 4.3 years ago by Dannon Baker270
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Comment: C: How To Become Admin On Galaxy Cloudman
... Thanks a lot, Enis! The problem is solved! Best regards, Yan 发件人: Enis Afgan [mailto:afgane@gmail.com] 发送时间: Sunday, September 29, 2013 4:39 PM 收件人: Yan He 抄送: Galaxy-user 主题: Re: [galaxy-user] How to become admin on Galaxy Cloudman Hi Yan, On CloudMan's Admin page (i.e., /cloud/admin) you ...
written 4.3 years ago by Yan He240
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How To Become Admin On Galaxy Cloudman
... Hi all, I just established Galaxy Cloudman on Amazon EC2. I would like to add some tools in tool shed to to it. However, I need to be the admin to do this. Once I got into the galaxy cloudman, I had to register a new account and then log in. The admin interface (described in tool shed wiki) didn' ...
galaxy written 4.3 years ago by Yan He240 • updated 4.3 years ago by Enis Afgan620
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Variant Annotation In Gatk Tools
... Hi all, I am analyzing some targeted resequencing data. I was trying to use Variant Annotation tool under GATK after got .VCF file. But some error as following returned. Would you please help me to figure out what happened? Or this tool can only be used for some model organisms? Thanks a lot! ...
gatk written 4.3 years ago by Yan He240 • updated 4.3 years ago by Jennifer Hillman Jackson23k
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About "Slice Bam" Tool
... Hi Jen and other galaxy-users, I was using "Slice BAM" tool on Galaxy to get the alignment overlap with the targeted intervals. After I got the output BAM file, I used "flagstat" to get the detailed information of the output BAM file. What I got from "flagstat" is as following. "13704486 + 0 i ...
galaxy written 4.3 years ago by Yan He240 • updated 4.3 years ago by Jennifer Hillman Jackson23k
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How To Extract Geneid From Pileup File?
... Dear galaxy-users, I am working on a project to identify and genotype SNPs in targeted genes. I did some analysis using Galaxy. First, mapping to the genome with Bowtie. Second, identify SNPs using MPileup in SAMtools. When I got the pileup file, the SNP information is in which chromosome and wha ...
bam samtools mpileup bowtie alignment written 4.4 years ago by Yan He240 • updated 4.4 years ago by Jennifer Hillman Jackson23k
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Exome-Capture Sequencing Analysis Tools?
... Hi Jen and other Galaxy-users, I am working on exome-capture sequencing with NGS. I am wondering if there is a tool to identify SNPs on Galaxy? I would like to get SNP information (position and allele frequency ) for each gene. Any information is highly appreciated! Thanks! Best wishes, Ya ...
galaxy written 4.4 years ago by Yan He240 • updated 4.4 years ago by Jennifer Hillman Jackson23k
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Comment: C: Counts Of Mapped Reads For Each Gene?
... Hi Anto, Thanks so much! I will try. Best wishes, Yan 发件人: Anto Praveen Rajkumar Rajamani [mailto:APR@hum-gen.au.dk] 发送时间: Thursday, August 22, 2013 3:57 PM 收件人: Yan He; galaxy-user@lists.bx.psu.edu 主题: RE: [galaxy-user] Counts of mapped reads for each gene? Hi Yan, I also had proble ...
written 4.4 years ago by Yan He240
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Comment: C: Counts Of Mapped Reads For Each Gene?
... Hi Anto, Thank you very much for your reply! I tried Galaxy/NBIC. However, I had problem with uploading my files. I used FTP, because the file I had was larger than 2G, but I couldn’t connect to the NBIC FTP. Do you have some idea how to solve the problem? Thanks! Yan 发件人: Anto Praveen Rajkumar ...
written 4.4 years ago by Yan He240
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Counts Of Mapped Reads For Each Gene?
... Hi Jen and other galaxy-users, I am analyzing our RNA-seq data. First, I mapped the RNA-seq data to the reference genome. I am wondering if there is a tool that could count the number of reads that mapped to each gene. That's important information for my subsequent analysis. Any reply is highly a ...
galaxy written 4.4 years ago by Yan He240 • updated 4.4 years ago by Anto Praveen Rajkumar Rajamani80

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