User: Mark Ebbert

gravatar for Mark Ebbert
Mark Ebbert70
Reputation:
70
Status:
Trusted
Location:
United States
Last seen:
6 months, 1 week ago
Joined:
3 years, 11 months ago
Email:
m******@gmail.com

Posts by Mark Ebbert

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Help with WGCNA pickSoftThreshold error
... Saved me here. That would have taken me a long time to figure out. ...
written 8 months ago by Mark Ebbert70
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2
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Comment: C: Problem with Haploview loading of files from latest (Sept 15-17 2014) update to
... Hey Scott, did you ever figure this out? ...
written 3.0 years ago by Mark Ebbert70
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6
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6
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Comment: C: Get Rs Number Based On Position
... Hey, Is there a good way to exclude rsIDs that have been merged? Thanks! ...
written 3.2 years ago by Mark Ebbert70
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1
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Answer: A: dbGaP, error downloading files
... The SRA "help desk" just got back to me. Sounds like there was an issue on their end because they told me to try the download again. I didn't need to change anything on my end. Hope this helps someone else down the road.     ...
written 3.2 years ago by Mark Ebbert70
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Comment: C: dbGaP, error downloading files
... Yup, thanks for your help. prefetch -X 1000G cart_201504091717.krt ...
written 3.2 years ago by Mark Ebbert70
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Comment: C: dbGaP, error downloading files
... Thank you for the suggestion. It fails for all of the files in my "cart" file. Only one of those even began downloading. I also just tried getting completely new samples in my cart file. They're all failing with a new error: 2015-04-14T19:59:48 prefetch.2.4.5 int: path corrupt while resolving tree ...
written 3.2 years ago by Mark Ebbert70
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1
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2.9k
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1
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dbGaP, error downloading files
... Hi, I'm trying to download some data in dbGaP. I setup the SRA toolkit per the description and began a download. Everything was working great, but I canceled the download (CTRL-C) so I could start a  screen session and restart the download. Rather, I wanted to log out of the machine without losing ...
software error dbgap written 3.2 years ago by Mark Ebbert70
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Comment: C: Picard MarkDuplicates error after using bamaddrg: "bin field of BAM record does
... Super helpful, thanks lomereiter! We opted for the first option and it worked great. ...
written 3.8 years ago by Mark Ebbert70
5
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1
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3.1k
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Picard MarkDuplicates error after using bamaddrg: "bin field of BAM record does not equal value computed..."
... Hi, We have a lot of bams from data that was sequenced and aligned before we received it. All of the bams are missing the read group (@RG) in the reads even though the read group is defined in the header. We ran `bamaddrg` (https://github.com/ekg/bamaddrg) to add the read groups to all reads and it ...
picard markduplicates sam validation error written 3.8 years ago by Mark Ebbert70 • updated 3.8 years ago by lomereiter410
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Comment: C: Tool to unmark duplicates
... Thank you for the reminder. My colleague and I were both looking for a solution and it looks like he also posted a question about it. Please excuse the duplicate post. Edit: Thank you everyone for your helpful responses! ...
written 3.9 years ago by Mark Ebbert70

Latest awards to Mark Ebbert

Popular Question 2.9 years ago, created a question with more than 1,000 views. For Tool to unmark duplicates
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Picard MarkDuplicates and SamTools rmdup algorithm documentation
Scholar 3.2 years ago, created an answer that has been accepted. For A: dbGaP, error downloading files
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Picard MarkDuplicates and SamTools rmdup algorithm documentation
Student 3.6 years ago, asked a question with at least 3 up-votes. For Tool to unmark duplicates

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