Moderator: John

gravatar for John
John11k
Reputation:
11,430
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Trusted
Location:
Germany
Website:
http://at.cg/
Last seen:
1 week, 3 days ago
Joined:
5 years, 10 months ago
Email:
m***********@gmail.com

Mistakes will be made...

Posts by John

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Comment: C: Amzon EC2 for bioinformatics, genomics, NGS analysis
... The vast majority of what AWS offers is unrelated to bioinformatic analysis. I give lot of examples in the first two paragraphs of the above, like DNS, SSL, etc. These are features that businesses and SMCs will pay a premium for, because setting that stuff up on your own is a real hassle. I was also ...
written 29 days ago by John11k
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Comment: C: Declining quality of biostars
... I think you'd need to really dramatically change the way threads are ordered on the main page, not ordered by time posted or time since last activity, but by using an algorithm much like Facebook's to push to the top of the page threads the site wishes users to see - perhaps because they are logged ...
written 9 weeks ago by John11k
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Comment: C: BAM to CRAM to BAM
... Unfortunately, due to the number of different ways the same data can be stored in SAM/BAM/CRAM, checksums can not be used as a proxy for knowing what data is stored. Slight variations in compression would change the checksum without touching the data at all. SAM -> BAM and BAM -> SAM are not e ...
written 9 weeks ago by John11k
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Comment: C: samtools sorting and indexing
... You're very welcome - if you run into any more complications please don't hesitate to open another question :) ...
written 11 weeks ago by John11k
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Comment: C: samtools sorting and indexing
... Oh they changed the syntax to be explicit!? Finally :D ...
written 11 weeks ago by John11k
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Answer: A: samtools sorting and indexing
... I think you're over-thinking things :) You can only index BAM files on position, and only when the data is sorted by position to begin with (don't ask...) So to sort by position just do: samtools sort my.sam > my_sorted.bam Then index with samtools index my_sorted.bam It's as easy as ...
written 11 weeks ago by John11k
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Comment: C: Declining quality of biostars
... Agreed - looking through the unanswered questions they're mainly either duplicates of older questions, or do not provide enough detail. Also it's summer and so the quality of questions typically drops and/or becomes all about 'where is a good place to study bioinformatics', etc. Having said that, i ...
written 11 weeks ago by John11k
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Comment: C: SAM file size after STAR alignment
... There are so many variables here it's impossible to say. If you didn't get an error then presumably you're fine. The file size increase is perfectly normal. But by the sounds of things you really should look into pairing-up with someone who knows what is going on to teach you the ropes :) ...
written 12 weeks ago by John11k
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Comment: C: Where and how NGS techniques are heading for the next 5 years?
... It's depressing that someone green-lighted funding for a project to encode and read DNA using current-day technology. Might as well set the money on fire. They both just made an encoding and then synthesized a ton of short fragments with indexes like disk inodes and called it a day. Very disappointi ...
written 3 months ago by John11k
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Comment: C: Meta-Analysis chip-seq data
... What do you define as a "meta-analysis"? ...
written 3 months ago by John11k

Latest awards to John

Popular Question 18 days ago, created a question with more than 1,000 views. For Create your own VPN to access work resources from home
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Why can't we downvote on this forum?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Create your own VPN to access work resources from home
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: I have to learn another language, but which one?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Create your own VPN to access work resources from home
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Create your own VPN to access work resources from home
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Are Lots Of Bioinformaticians Embedded In Wet Labs? Any Ideas On Sources Of Demo
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Create your own VPN to access work resources from home
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Are Lots Of Bioinformaticians Embedded In Wet Labs? Any Ideas On Sources Of Demo
Scholar 11 weeks ago, created an answer that has been accepted. For A: samtools : print single columns at position
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: I have to learn another language, but which one?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Why can't we downvote on this forum?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Are Lots Of Bioinformaticians Embedded In Wet Labs? Any Ideas On Sources Of Demo
Appreciated 3 months ago, created a post with more than 5 votes. For A: PhD in bioinformatics or biostatistics as a wet-lab scientist?
Popular Question 3 months ago, created a question with more than 1,000 views. For Create your own VPN to access work resources from home
Popular Question 4 months ago, created a question with more than 1,000 views. For Create your own VPN to access work resources from home
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Why can't we downvote on this forum?
Appreciated 4 months ago, created a post with more than 5 votes. For A: PhD in bioinformatics or biostatistics as a wet-lab scientist?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Why can't we downvote on this forum?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Are Lots Of Bioinformaticians Embedded In Wet Labs? Any Ideas On Sources Of Demo
Appreciated 4 months ago, created a post with more than 5 votes. For A: PhD in bioinformatics or biostatistics as a wet-lab scientist?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: I have to learn another language, but which one?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: I have to learn another language, but which one?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Are Lots Of Bioinformaticians Embedded In Wet Labs? Any Ideas On Sources Of Demo
Scholar 4 months ago, created an answer that has been accepted. For A: samtools : print single columns at position

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