User: igor

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igor3.9k
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Posts by igor

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Comment: C: StackExchange/Area51 bioinformatics is back
... If you cross-link, then people from both communities will assume that the other community will provide the answer. At least that's a common assumption (would be nice to test how valid this claim is). Also, you can argue cross-linking is disrespectful of other people's time as well. You expect every ...
written 17 hours ago by igor3.9k
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Answer: A: Picard vs samtools rmdup
... This previous thread about the exact differences between Samtools and Picard duplicate removal might be helpful: https://www.biostars.org/p/105291/ Also, this really old thread: http://seqanswers.com/forums/showthread.php?t=5424 ...
written 2 days ago by igor3.9k
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Comment: C: Results of various counting scripts
... Exactly. featureCounts needs an extra `-p` flag. ...
written 6 days ago by igor3.9k
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Answer: A: Mutation processing by cbioportal
... There are differences in variant reporting between the old TCGA Data Portal and the new GDC. I think there was a discussion here a few weeks ago about the differences, but I can't find it now. I believe cBioPortal is still using the old TCGA data and applying their own filters: > The TCGA provi ...
written 6 days ago by igor3.9k
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Answer: A: Reshape tabular data frame to wide format
... You don't need to do it manually. Try the `tidyr` `spread()` function: http://tidyr.tidyverse.org/reference/spread.html ...
written 6 days ago by igor3.9k
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Comment: C: StackExchange/Area51 bioinformatics is back
... > How many of us went into Bioinformatics because we're real particular > about our user interfaces? Bioinformatics as a community should probably be more concerned about user interfaces. Definitely lots of room for improvement there. ...
written 7 days ago by igor3.9k
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Comment: C: StackExchange/Area51 bioinformatics is back
... Not sure the open source argument works. If someone takes an open source project and fixes a bug or forks the code to make an improved tool, the world is slightly better and everyone is happier. If someone makes a new Biostars, it's a big mess (see this post). Biostars is not a software. It's a com ...
written 7 days ago by igor3.9k
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Comment: C: How to extract only continuously aligned reads from a SAMfile
... See this discussion about split reads: https://www.biostars.org/p/146178/ That might be what you are looking for. ...
written 8 days ago by igor3.9k
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Comment: C: How to extract only continuously aligned reads from a SAMfile
... Have you considered trimming the reads to 50bp, for example? Those would be far less likely to be chimeric. It might be easier and more productive than throwing out all the problematic ones (assuming that most reads are affected). ...
written 9 days ago by igor3.9k
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counting sequences with fuzzy uniq (with mismatches)
... You can run `uniq -c` to count occurrences of unique strings. Is there a way to do that accounting for mismatches? If these are sequencing reads, then you may expect mismatches. For example, for `grep`, there is a `agrep` ("approximate GREP for fast fuzzy string searching"). ...
cli unix written 9 days ago by igor3.9k

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Commentator 4 days ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
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Popular Question 14 days ago, created a question with more than 1,000 views. For Best way to perform single-cell RNA-seq normalization
Scholar 4 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
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Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
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Scholar 6 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
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