Moderator: lh3

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lh328k
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1 day ago
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6 years, 5 months ago
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Posts by lh3

<prev • 1,452 results • page 1 of 146 • next >
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Answer: A: BWA mem output inconsistent on same but re-ordered FASTQ input
... There are two sources of randomness. The first is caused by the insert size estimate. Different batches of reads have slightly different insert size distribution, which affects paired-end alignment. You can in principle feed the insert size distribution to bwa-mem, but the bwa-mem estimate is usuall ...
written 29 days ago by lh328k
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1
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Comment: C: Can't import HTSeq module in python promt
... You have two versions of libstdc++, one from the system and the other from conda. Apparently, you compiled HTSeq with the system libstdc++, but the library found the conda version when running. The solution depends on how much you use conda and your system configuration. Hard to say without seeing t ...
written 3 months ago by lh328k
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Comment: C: How to retrieve BAM file from NCBI SRA
... Don't know what is happening now. At least before, they only provided aligned cSRA files, not BAMs. ERA should have BAMs if submitters uploaded them. ...
written 3 months ago by lh328k
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files
... Great work. Talking about fastq compression, it is worth mentioning [this paper](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0059190), and fqzcomp and dsrc in particular. ...
written 3 months ago by lh328k
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Comment: C: Why annotations are not encoded using standard informatic format ?
... It is not a standard. Its github repo is flagged by few. GA4GH of course knew this thing, but quickly ruled it out. I also find defining a json schema with json is very awkward. ...
written 3 months ago by lh328k
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Comment: C: Why annotations are not encoded using standard informatic format ?
... Genbank format may predate JSON by a decade or so, when most Unix tools crashed if there was a line longer than 1024 bytes. ...
written 3 months ago by lh328k
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Answer: A: Why annotations are not encoded using standard informatic format ?
... In addition to what others said, JSON is primarily a serialization format. We do not have an official standard to formally define JSON schemas. Without a schema specifying field names and types, a program won't be able to retrieve data. This problem seems small but bites you hard when you go down to ...
written 3 months ago by lh328k
0
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Comment: C: How do people know to use at least 30X coverage in WGS?
... Illumina has been talking about quality binning for over six years. I have seen multiple lines of evidence from Illumina, Broad, Sanger and my own experiment that quality binning has little to do with the quality of variant calling for human data. I rarely work with nextseq data. I did hear complain ...
written 4 months ago by lh328k
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Comment: C: Why is this insertion detected by NGS a false positive ?
... IonTorrent is just bad at tiny indels. I bet it is a sequencing problem rather than an informatics problem. ...
written 4 months ago by lh328k
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Comment: C: is there an Mappers/aligners working on adam sequencing data
... When you say "slow", is it because the alignment itself is slow, or because conversion to fastq is slow? If it is former, use SNAP; if latter, you should stream fastq to the mapper – most mainstream mappers can read fastq from stdin – instead of writing the actual fastq to disk. ...
written 5 months ago by lh328k

Latest awards to lh3

Appreciated 24 days ago, created a post with more than 5 votes. For Why is academic software hard to install?
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Efficient Python data structure to store and process annotations
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Why You Need Perl/Python If You Know R/Shell [Ngs Data Analysis]
Scholar 6 weeks ago, created an answer that has been accepted. For A: Coordinates of the PAR3 Region on chrX and chrY
Appreciated 7 weeks ago, created a post with more than 5 votes. For Aligning Sequence Reads, Clone Sequences And Assembly Contigs With Bwa-Mem
Appreciated 7 weeks ago, created a post with more than 5 votes. For Why is academic software hard to install?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Efficient Python data structure to store and process annotations
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Efficient Python data structure to store and process annotations
Appreciated 3 months ago, created a post with more than 5 votes. For Why is academic software hard to install?
Scholar 3 months ago, created an answer that has been accepted. For A: Coordinates of the PAR3 Region on chrX and chrY
Appreciated 3 months ago, created a post with more than 5 votes. For Why is academic software hard to install?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Remotely Access Bigwig File With Python
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Samtools + Picard Markduplicates
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: How To Split A .Vcf.Gz File
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Efficient Python data structure to store and process annotations
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Variation & Genotype Calling From Ngs Data - Per Sample Or Multi Sample?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Remotely Access Bigwig File With Python
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Variation & Genotype Calling From Ngs Data - Per Sample Or Multi Sample?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Why You Need Perl/Python If You Know R/Shell [Ngs Data Analysis]
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Why You Need Perl/Python If You Know R/Shell [Ngs Data Analysis]
Appreciated 7 months ago, created a post with more than 5 votes. For A: Why You Need Perl/Python If You Know R/Shell [Ngs Data Analysis]
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Why You Need Perl/Python If You Know R/Shell [Ngs Data Analysis]
Scholar 7 months ago, created an answer that has been accepted. For A: Coordinates of the PAR3 Region on chrX and chrY
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Java or C++ (which side should I choose)
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Combining The Paired Reads From Illumina Run

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