User: Macspider

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Macspider2.8k
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Posts by Macspider

<prev • 534 results • page 1 of 54 • next >
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Comment: C: Interpretation of Trimmomatic Results after Paired-End Adapter Trimming
... It depends on how your library was generated, and that you should ask to who made the sequencing libraries. If they used TruSeq2 and you're using the TruSeq3 file, then you should change that. Check the files available in the `Trimmomatic` install directory. ...
written 19 days ago by Macspider2.8k
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Answer: A: How do I Creat count table from raw seqdata ( fastq) and run Deseq2?
... Map your reads with your mapping software of choice (just needs to output a sam file) and then run that sam file through a feature counter, for example [HTSeq][1]. [1]: https://htseq.readthedocs.io/en/release_0.11.1/ ...
written 5 weeks ago by Macspider2.8k
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Comment: C: Bowtie2 mapped just 50% of the reads
... Is your library stranded? ...
written 5 weeks ago by Macspider2.8k
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Answer: A: Extracting divergence times from 4DTv
... I'm answering myself, for future readers: The 4DTv ratio cannot be converted into millions of years, as it is a relative measure of time and therefore can't be converted into an absolute one. However, one can use the *rate of substitution at neutrally evolving sites* to determine age. Basically: ...
written 8 weeks ago by Macspider2.8k
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Comment: C: Trimmomatic: LEADING and TRAILING
... Also, there is no such thing as "what it should be". It depends on the data, on the quality of your sequencing, on the risks you're willing to take. Thresholds are just something *we* put, but they don't define perfection. What is important, is that you understand the rationale behind it in order to ...
written 8 weeks ago by Macspider2.8k
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Answer: A: Trimmomatic: LEADING and TRAILING
... Trimmomatic will trim bases at the beginning (i.e. "LEADING") or at the end ("TRAILING") of your read if their quality score falls below the value specified after the colon (":"). Have a look at their manual: http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pd ...
written 8 weeks ago by Macspider2.8k
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Comment: C: ETE3 TreeError: 'Nodes are not connected!': how to fix?
... It's pretty weird: I started `except`-ing the error to get those trees, and now it is not showing that error anymore. I have no clue on how to reconstruct the previous situation. Perhaps there was some I/O error and something got read/written wrongly from/to the file? I don't know what to think anym ...
written 8 weeks ago by Macspider2.8k
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Comment: C: ETE3 TreeError: 'Nodes are not connected!': how to fix?
... Not that I know of. All these trees worked in all my analyses, it would be very unexpected. ...
written 8 weeks ago by Macspider2.8k
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ETE3 TreeError: 'Nodes are not connected!': how to fix?
... Hi everyone, I am working with ETE3 and I stumbled upon an error that I have never retrieved before: ete3.coretype.tree.TreeError: 'Nodes are not connected!' The error seems to trace back to the `get_common_ancestor()` function, which is in the `tree.py` script of ETE3. The lines raising ...
nodes phylogenetics phylome treeerror ete written 8 weeks ago by Macspider2.8k
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Extracting divergence times from 4DTv
... Hello everyone, I have just finished generating a 4DTv plot ([example][1]) for paralog and ortholog genes in a project I'm working on. While reading some papers where they also have made such a plot (listed in the introduction [here][2]), I see that many times they estimate divergence times betwee ...
substitution variants time 4dtv divergence written 3 months ago by Macspider2.8k

Latest awards to Macspider

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Scholar 8 weeks ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 3 months ago, created a question with more than 1,000 views. For DESeq2 proper design setting
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How to add tophat and bowtie to the path?
Great Question 3 months ago, created a question with more than 5,000 views. For Best way to compare two samples in a VCF file
Appreciated 3 months ago, created a post with more than 5 votes. For A: Explanation of a Perl script
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: How to add tophat and bowtie to the path?
Scholar 5 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Good Question 8 months ago, asked a question that was upvoted at least 5 times. For Best way to compare two samples in a VCF file
Popular Question 8 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Popular Question 9 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 12 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Appreciated 13 months ago, created a post with more than 5 votes. For Best way to compare two samples in a VCF file
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 13 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 14 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 14 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 15 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 15 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 16 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?

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