User: Bao Ho

gravatar for Bao Ho
Bao Ho80
Reputation:
80
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Trusted
Location:
UCSF
Last seen:
1 year, 6 months ago
Joined:
2 years, 2 months ago
Email:
h******************@gmail.com

Posts by Bao Ho

<prev • 12 results • page 1 of 2 • next >
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Answer: C: Current history is unreachable
... Server/connection issues usually occur during heavy traffic. Several projects of mine are still waiting to run. It is slightly inconvenient but I was expecting a long queue today because it is Monday. You can check back later today or tomorrow and see if the problem persists. Sometime we just have t ...
written 18 months ago by Bao Ho80
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Comment: C: MACS2 peak calling error
... There isn't enough information to troubleshoot your issue. Can you share your history? - Bao ...
written 18 months ago by Bao Ho80
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Answer: A: transferring bewtween two remote sites
... If you can access your remote computer through ssh (I personally use putty), you can upload your data to galaxy through the FTP function. Simply navigate to the remote directory that contains the files that you want to upload, then type > ftp usegalaxy.org You will be prompted to input your ac ...
written 20 months ago by Bao Ho80
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Comment: C: Uploading data to galaxy
... Hi, Has the "leave .gz files compressed" function/policy been disabled? I have just uploaded a batch of gzip files and they were automatically decompressed to my surprise. Bao ...
written 20 months ago by Bao Ho80
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Comment: C: ChiP Seq Track height and scaling in UCSC Browser
... Thank you! I will try to make output from MACS and MACS2 consistent & similar. I will report my further findings later. ...
written 20 months ago by Bao Ho80
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Answer: A: How can I see the amount of reads and aligned reads from Bowtie?
... You can use Flagstat on your alignment results (SAM/BAM). This is an example of the text file result that I get from Flagstat: > 30407764 + 0 in total (QC-passed reads + QC-failed reads) > 0 + 0 secondary > 0 + 0 duplicates > 19468353 + 0 mapped (64.02%:-nan%) > 0 + 0 pair ...
written 20 months ago by Bao Ho80
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Comment: C: ChiP Seq Track height and scaling in UCSC Browser
... I have tried to run MACS and MACS2 on the same alignment result for several data sets. Surprisingly the results I received are very similar. In some cases MACS2 yielded a higher level of noise/background. It seems that the data that I shared above is the only unique case with tiny peaks and clean ba ...
written 20 months ago by Bao Ho80
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ChiP Seq Track height and scaling in UCSC Browser
... Hi all, I recently work on several ChIP-seq data sets. My traditional workflow is .fastq/.fastq.gz -> .sam (via Bowtie) -> MACS (after BAM conversion) -> wig to bigwig conversion. Thus, my usual output are .bw track files that I then view through UCSC genome browser, with the y axis (track ...
macs2 macs bigwig viz ucsc written 20 months ago by Bao Ho80 • updated 20 months ago by Jennifer Hillman Jackson25k
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Server crash? "Unable to run this job due to a cluster error"
... I was working on several ChIP seq projects when the public Galaxy server suddenly crashed around 5-6pm yesterday, Pacific Time (I could not connect to usegalaxy.org, my browser would say "Connection Timeout"). When the server came back up all item that had been running before became red (error/halte ...
chip-seq galaxy software error written 20 months ago by Bao Ho80 • updated 20 months ago by Jennifer Hillman Jackson25k
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Comment: C: Galaxy failed to unzip gz files after uploading
... Hi, I was hoping that what you described was that case. But when I uploaded my fastq.gz files and run Bowtie with them as input (this is a part of a workflow), Bowtie failed to run and this is the error message: Error aligning sequence. Error: reads file does not look like a FASTQ file terminate c ...
written 20 months ago by Bao Ho80

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