User: Wjeck
Wjeck • 480
- Reputation:
- 480
- Status:
- Trusted
- Location:
- Chapel Hill, NC
- Website:
- http://onconomicon.blo...
- Last seen:
- 10 months ago
- Joined:
- 10 years, 6 months ago
- Email:
- w***********@gmail.com
MD/PhD student at University of North Carolina at Chapel Hill
Posts by Wjeck
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0
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8
answers
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8
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... There is another possibility, which I don't see mentioned here, which is that the sequences may arise from stable lariat RNA. Stable lariats have been observed in polyA minus fractions of RNA, and could presumably be observed in incompletely selected polyA+ RNA.
...
written 8.0 years ago by
Wjeck • 480
1
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3
answers
3.4k
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3
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... Just a note, contrary to this post IGV does seem to be able to handle https and the associated encryption, but samtools does not.
...
written 8.4 years ago by
Wjeck • 480
0
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3
answers
3.4k
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3
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... Doesn't seem to work for me. I am not sure that samtools recognizes https is a web address. The response I get is:
open: No such file or directory
[main_samview] fail to open "https://uname:*******@website/my.bam" for reading.
(with my website, password etc, of course) ...
1
vote
2
answers
6.1k
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2
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... Not sure if this will work, but you could try to use the CDS start and CDS stop fields. I believe they are both equal to the Transcription start field for noncoding RNAs. For coding genes CDS start != CDS stop
...
written 8.4 years ago by
Wjeck • 480
13
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3
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3.4k
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8 follow
3
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... I am trying to pull regions from a bunch of BAM files on an online server. I'd like to pull the reads mapping to a certain 1kb or so chunk and download them for analysis. They are far too massive to download them all, and it's impractical even to wget them one at a time and pull the regions out usi ...
written 8.4 years ago by
Wjeck • 480
• updated
8 months ago by
Nicolas Rosewick ♦ 9.2k
0
votes
1
answer
4.2k
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1
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... This appears to be the answer: 4G is simply not enough to run indel realignment on a HiSeq lane. Quadrupled to 16G and am seeing better performance and no run failures (though I presume there is still the potential there for very deep sequencing). ...
written 9.2 years ago by
Wjeck • 480
4
votes
1
answer
4.2k
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1
answer
... I got the following rather strange error while running GATK indel realignment on a considerably larger file (HiSeq) than I am used to:
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.nio.HeapByteBuffer.<init>(HeapByteBuffer.java:39)
at java.ni ...
written 9.2 years ago by
Wjeck • 480
• updated
9.2 years ago by
biobot 0.0.77.a.1099 ♦ 6.1k
0
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6
answers
7.1k
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6
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... Added to the mix from KU and UNC collaboration: Mapsplice. This has proven extremely useful on top of the above for it's fusion detection capabilities. ...
written 9.2 years ago by
Wjeck • 480
1
vote
11
answers
165k
views
11
answers
... I use this method to calculate % of sites with at least a coverage of 20x in a list of sites from a bed. It provides that number directly as output. ...
written 9.5 years ago by
Wjeck • 480
5
votes
73
answers
34k
views
73
answers
... +1 for OS dependent line breaks. This still trips me up on occasion when I get files from other groups and find that (gasp) they use windows. ...
Latest awards to Wjeck
Popular Question
4.3 years ago,
created a question with more than 1,000 views.
For Best Spliced Aligner To Human Genome With Limited Rna-Seq Reads
Appreciated
5.7 years ago,
created a post with more than 5 votes.
For C: What Are The Most Common Stupid Mistakes In Bioinformatics?
Great Question
5.7 years ago,
created a question with more than 5,000 views.
For Best Spliced Aligner To Human Genome With Limited Rna-Seq Reads
Popular Question
5.7 years ago,
created a question with more than 1,000 views.
For Best Spliced Aligner To Human Genome With Limited Rna-Seq Reads
Appreciated
7.6 years ago,
created a post with more than 5 votes.
For Best Spliced Aligner To Human Genome With Limited Rna-Seq Reads
Appreciated
7.6 years ago,
created a post with more than 5 votes.
For Searching Ncbi'S Short Read Archive
Good Question
7.6 years ago,
asked a question that was upvoted at least 5 times.
For Best Spliced Aligner To Human Genome With Limited Rna-Seq Reads
Good Question
7.6 years ago,
asked a question that was upvoted at least 5 times.
For Searching Ncbi'S Short Read Archive
Good Answer
7.6 years ago,
created an answer that was upvoted at least 5 times.
For A: Rna-Seq Pipeline
Popular Question
7.6 years ago,
created a question with more than 1,000 views.
For Best Spliced Aligner To Human Genome With Limited Rna-Seq Reads
Popular Question
7.6 years ago,
created a question with more than 1,000 views.
For Searching Ncbi'S Short Read Archive
Popular Question
7.6 years ago,
created a question with more than 1,000 views.
For Gatk Indel Realignment Dies In A Memory Explosion... Any Fixes?
Supporter
7.6 years ago,
voted at least 25 times.
Commentator
7.6 years ago,
created a comment with at least 3 up-votes.
For C: What Are The Most Common Stupid Mistakes In Bioinformatics?
Teacher
7.6 years ago,
created an answer with at least 3 up-votes.
For A: T Cell Specific Gene Expression Data
Student
7.6 years ago,
asked a question with at least 3 up-votes.
For Best Spliced Aligner To Human Genome With Limited Rna-Seq Reads
Student
7.6 years ago,
asked a question with at least 3 up-votes.
For Searching Ncbi'S Short Read Archive
Student
7.6 years ago,
asked a question with at least 3 up-votes.
For Trying To Pull Regions From An Online Bam File Without Downloading
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