User: 杨继文

gravatar for 杨继文
杨继文210
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210
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New User
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Last seen:
5 years, 8 months ago
Joined:
5 years, 11 months ago
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j************@126.com

Posts by 杨继文

<prev • 19 results • page 1 of 2 • next >
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Tophat Mapping Error
... Hi all, I got the following error infomation during Tophat mapping An error occurred running this job: Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. Please let me know what's wrong. Help will ...
tophat rna-seq written 5.7 years ago by 杨继文210 • updated 5.7 years ago by Jennifer Hillman Jackson23k
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Jobs In Queue
... I have similar problems. My tophat job was sent 6 hours ago. Now the job is still waiting to be run. Jiwen Hi, My cufflinks jobs sat in the queued state for 12+ hours so I restarted them this morning. They've been in the queued state now for about 2-3 hours. Any idea why? Here's a link to my his ...
cufflinks rna-seq written 5.7 years ago by 杨继文210
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Help!!! Cuffdiff Log2 Value
... Hi, I am analyzing my RNA-Seq data. After running cuffdiff, I got a list of differentially expressed transcrpts or genes. As far as I know, log2 value = fold change. However, there are minus values. Is this possible?? log2 value can not be minus. Did I miss something?? Looking forward to your he ...
cuffdiff rna-seq written 5.7 years ago by 杨继文210 • updated 5.7 years ago by Jennifer Hillman Jackson23k
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Cuffcompare Or Cuffmerge
... Hi all, I read one paper "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks". They say the procedure for RNA-Seq analysis is Tophat-->cufflinks-->cuffmerge-->cuffdiff But what I normally do in Galaxy is Tophat-->cufflinks-->cuffcomp ...
cufflinks cuffmerge rna-seq written 5.8 years ago by 杨继文210 • updated 5.8 years ago by ericliaowei@gmail.com70
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Mapping Paired End Reads With Tophat
... Hi all, After mapping, I used IGV to have a look at the mapping. There are a lot of mapped reads without pair reads. Should I keep these reads? or Is this a problem for cufflinks analysis? What I tried is: 1. BAM to SAM 2. Filter SAM: set Read mapped in a proper pair to Yes. The result is that o ...
cufflinks rna-seq written 5.8 years ago by 杨继文210 • updated 5.7 years ago by Jennifer Hillman Jackson23k
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Tophat Mapping
... Hi, After mapping RNA-Seq paired end reads with Tophat, I can see that most of reads fall into the right regions. However, I still can see lots of reads mapped to non-coding region (the locations where the reads are mapped to don't contain exons). I am wondering if these "non-coding reads" will ...
cufflinks rna-seq written 5.8 years ago by 杨继文210 • updated 5.8 years ago by Jeremy Goecks2.2k
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Help!! Tophat Paired End Reads
... Hi, I am very confused by my mapping. Please help me figure out what's wrong with my operation. I got Illumina Hiseq 2000 paired end reads (mouse), and I used Tophat to map these reads. After mapping, I used IGV to have a look at the mapping. I can see that some of the reads fall into exons or spa ...
tophat rna-seq written 5.8 years ago by 杨继文210 • updated 5.8 years ago by Jennifer Hillman Jackson23k
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Help!! Uploading With Ftp
... Hi, I am uploading files to Galaxy via FTP. The speed is only 30kb/sec. Is there something wrong with my operation? or is this just normal due to Galaxy's work load? Looking forward to your answers. Thanks Jiwen ...
galaxy written 5.8 years ago by 杨继文210 • updated 5.8 years ago by Jennifer Hillman Jackson23k
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Tophat Paired End Read
... Hi all, I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate files. Before mapping, I need to trim the reads. My questions is : Do I have to join pair end reads before timming, and then split again for Tophat??? Lookiong forward to your answers. Thanks Jiwen ...
tophat rna-seq written 5.8 years ago by 杨继文210 • updated 5.8 years ago by Jennifer Hillman Jackson23k
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Job Running Speed Is Really Slow
... Dear Galaxy team, I found glalaxy (website) is running really slow today. I just did some text manipulations over a very small file. It takes a long time till the gray colour (waiting) turns into yellow (running). Now the jobs are still waiting to be processed (gray colour). I have to analyze my R ...
galaxy written 5.9 years ago by 杨继文210 • updated 5.9 years ago by Jennifer Hillman Jackson23k

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