Moderator: John
John ♦ 11k
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Posts by John
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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 2 days ago by
John ♦ 11k
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2
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159
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2
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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 2 days ago by
John ♦ 11k
0
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210
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1
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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 18 days ago by
John ♦ 11k
0
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210
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1
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Comment:
C: samtools sorting and indexing
... Oh they changed the syntax to be explicit!? Finally :D ...
written 18 days ago by
John ♦ 11k
3
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1
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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 19 days ago by
John ♦ 11k
0
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5
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808
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5
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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 19 days ago by
John ♦ 11k
1
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1
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... 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 20 days ago by
John ♦ 11k
3
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6
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443
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6
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... 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 5 weeks ago by
John ♦ 11k
1
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1
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161
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1
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Comment:
C: Meta-Analysis chip-seq data
... What do you define as a "meta-analysis"? ...
written 5 weeks ago by
John ♦ 11k
2
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2
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484
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2
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... Yeah you add the numbers together for the ones you want to keep (-f), and the ones you want to remove (-F). A good tool to figure this out is [Explain SAM flags][1]. I don't remember any of these numbers off by heart, i use that tool to work it out each time. The "0x..." notation you were using befo ...
written 6 weeks ago by
John ♦ 11k
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