Moderator: lh3

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lh329k
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Posts by lh3

<prev • 1,489 results • page 1 of 149 • next >
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Comment: C: Are these false somatic variants? Visual inspection with IGV
... 29 is pretty low. A blat score 300 is high enough to make me worry. What is coordinate of this region? The genome build? ...
written 1 day ago by lh329k
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Comment: C: Are these false somatic variants? Visual inspection with IGV
... In somatic mutation calling, multiple SNVs on one read are mostly false positives even if you see no evidence in the paired normal. I am not sure what is the exact cause, but most SNVs like these don't get validated experimentally. ...
written 1 day ago by lh329k
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Comment: C: Selecting Random Pairs From Fastq?
... Yes, as long as you use the same -s. ...
written 2 days ago by lh329k
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Comment: C: Variant annotation and filtration server ALAPY Genome Explorer (AGx)
... Most biologists don't run VM, let alone install a Linux in it. Your tool should simplify data processing, not complicate it. I don't know what industrial users will think about the tool, but I am moderately certain that few academia users will use it. The dependencies you chose are too heavy. I don ...
written 3 days ago by lh329k
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Comment: C: Are these false somatic variants? Visual inspection with IGV
... Likely false. To confirm that, you need to look at the mapping quality of reads with mismatches. ...
written 3 days ago by lh329k
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Comment: C: Variant annotation and filtration server ALAPY Genome Explorer (AGx)
... This will be an interesting tool. However, all the clusters I have access to disallow users to run docker, let alone the root permission. If you are requiring apt-get and using docker, you have excluded several thousand potential users working on these clusters. If you want your tool to be widely us ...
written 4 days ago by lh329k
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Answer: A: Software for Tree Visualization
... See my old answer [here](https://www.biostars.org/p/2438/). ...
written 6 days ago by lh329k
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Comment: C: BWA: Why paired reads mapped to different chromosome?
... Another leading cause is artifacts in library prep. ...
written 11 days ago by lh329k
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Comment: C: picard MarkDuplicates find EOF problem
... Run `samtools view -H your.bam > /dev/null` on all your bams. If you see "EOF marker is absent" for all your bams, they must have been produced by ancient tools, which would really surprise me nowadays – EOF marker was added over 5 years ago. If some of them yields the warning but others not, the ...
written 12 days ago by lh329k
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Comment: C: picard MarkDuplicates find EOF problem
... Your BAM is really incomplete/corrupted. You will lose data even if you manage to bypass picard's sanity check. You need to re-download or re-process it. ...
written 12 days ago by lh329k

Latest awards to lh3

Appreciated 6 days ago, created a post with more than 5 votes. For Why is academic software hard to install?
Commentator 6 days ago, created a comment with at least 3 up-votes. For C: Remotely Access Bigwig File With Python
Appreciated 6 days ago, created a post with more than 5 votes. For A: Why You Need Perl/Python If You Know R/Shell [Ngs Data Analysis]
Appreciated 8 days ago, created a post with more than 5 votes. For Why is academic software hard to install?
Commentator 16 days ago, created a comment with at least 3 up-votes. For C: Remotely Access Bigwig File With Python
Good Answer 20 days 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 20 days ago, created a post with more than 5 votes. For Why is academic software hard to install?
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Efficient Python data structure to store and process annotations
Commentator 24 days ago, created a comment with at least 3 up-votes. For C: Remotely Access Bigwig File With Python
Commentator 24 days ago, created a comment with at least 3 up-votes. For C: How To Liftover Genomic Regions From Dm3 (Drosophila) To Mm9 (Mouse)
Scholar 4 weeks ago, created an answer that has been accepted. For A: Coordinates of the PAR3 Region on chrX and chrY
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Efficient Python data structure to store and process annotations
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Remotely Access Bigwig File With Python
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Remotely Access Bigwig File With Python
Appreciated 5 weeks ago, created a post with more than 5 votes. For Why is academic software hard to install?
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: Remotely Access Bigwig File With Python
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Efficient Python data structure to store and process annotations
Appreciated 12 weeks ago, created a post with more than 5 votes. For Why is academic software hard to install?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Efficient Python data structure to store and process annotations
Good Answer 3 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]
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?
Appreciated 3 months ago, created a post with more than 5 votes. For Aligning Sequence Reads, Clone Sequences And Assembly Contigs With Bwa-Mem
Teacher 4 months 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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