Moderator: lh3

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lh329k
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Posts by lh3

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Comment: C: StackExchange/Area51 bioinformatics is back
... You are used to the forum-like biostar – you want to discuss a lot in comments. In a proper Q&A format, if you think you know better on this genome assembly problem, provide another answer. Explain clearly why it is better than other alternatives and let users play the judge. When someone reach ...
written 1 day ago by lh329k
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Comment: C: StackExchange/Area51 bioinformatics is back
... I think many people criticizing SE are generalizing their experiences in stack overflow (SO) to SE. SO is over crowded and diversified. It is a hell to newcomers. However, many focused SE communities are fairly friendly. If you look at the [biology SE](https://biology.stackexchange.com), you can see ...
written 1 day ago by lh329k
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Comment: C: StackExchange/Area51 bioinformatics is back
... I am a [long time supporter of downvote](https://www.biostars.org/p/74381/) and played an important role in [bringing back post closing](https://www.biostars.org/p/73420/) (though biostar still lacks the vote-to-close feature). Many early biostar users also [favored downvote](https://groups.google.c ...
written 1 day ago by lh329k
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Comment: C: StackExchange/Area51 bioinformatics is back
... IIRC, in 2012/2013 when someone argued biostar comments are superior to SE, I said something like (couldn't find the thread): it is not because SE doesn't have the manpower to implement nested comments; it is because such comments are distracting. SE also puts a 512-character hard limit on comments, ...
written 1 day ago by lh329k
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Comment: C: NGS files' shrinkage software: ALAPY Compressor, only fastq files so far =)
... I believe most people would easily choose a format ready for both archive and analysis purposes over an archive only format, especially when there is a ~20X performance gap. So far as I know, most large sequencing centers discard raw fastq. Converting a sorted bam/cram to unsorted fastq with samtool ...
written 12 days ago by lh329k
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Comment: C: NGS files' shrinkage software: ALAPY Compressor, only fastq files so far =)
... It is Hiseq. It is also important to include human WGS data sets. On compression, the top requirement is stream-ability. i.e. you start to get output without reading the whole input file or a significant portion of the file. This way, you can pipe the result to downstream tools without explicitly g ...
written 14 days ago by lh329k
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Answer: A: NGS files' shrinkage software: ALAPY Compressor, only fastq files so far =)
... So, I decided to do an evaluation myself. The input file is from [GAGE-B](https://ccb.jhu.edu/gage_b/datasets/index.html). I am looking at "Mycobacterium abscessus 6G-0125-R". I created an interleaved fastq from two ends. The fastq covers the reference genome for a few hundred folds approximately. H ...
written 16 days ago by lh329k
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Comment: C: NGS files' shrinkage software: ALAPY Compressor, only fastq files so far =)
... As I commented in some other thread, on FASTQ compression, the state of art is represented by [this paper](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0059190). Any new tools should be compared to it. This paper is worth reading. It is in fact reporting the results of a [coding ...
written 16 days ago by lh329k
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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 8 weeks ago by lh329k
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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 lh329k

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Commentator 1 day ago, created a comment with at least 3 up-votes. For C: Remotely Access Bigwig File With Python
Appreciated 1 day ago, created a post with more than 5 votes. For Why is academic software hard to install?
Commentator 15 days ago, created a comment with at least 3 up-votes. For C: Remotely Access Bigwig File With Python
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Efficient Python data structure to store and process annotations
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
Good Answer 8 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 10 weeks ago, created an answer that has been accepted. For A: Coordinates of the PAR3 Region on chrX and chrY
Appreciated 11 weeks ago, created a post with more than 5 votes. For Why is academic software hard to install?
Appreciated 11 weeks ago, created a post with more than 5 votes. For Aligning Sequence Reads, Clone Sequences And Assembly Contigs With Bwa-Mem
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Efficient Python data structure to store and process annotations
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Scholar 4 months ago, created an answer that has been accepted. For A: Coordinates of the PAR3 Region on chrX and chrY
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Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Remotely Access Bigwig File With Python
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Samtools + Picard Markduplicates
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Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Variation & Genotype Calling From Ngs Data - Per Sample Or Multi Sample?
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