User: Macspider

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Macspider3.0k
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Vienna - BOKU
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macspider_music
Last seen:
6 days, 8 hours ago
Joined:
3 years, 8 months ago
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Posts by Macspider

<prev • 567 results • page 1 of 57 • next >
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Comment: C: Choice between Nanopore cDNA or direct RNA sequencing
... True. Thanks for the point of view! ...
written 13 days ago by Macspider3.0k
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Comment: C: Choice between Nanopore cDNA or direct RNA sequencing
... We do have ample sample and we have enough budget. The most crucial part is to choose a path that returns sufficient results because a person in the project has limited time to complete their part of the analysis :) ...
written 13 days ago by Macspider3.0k
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Choice between Nanopore cDNA or direct RNA sequencing
... Hi everyone, I am exploring the possibilities I have for an RNA meta-transcriptomic sequencing experiment involving Nanopore. Disclaimer #1: I'm a bioinformatician, so I don't have much wet lab background to choose a couple of things in my workflow. Disclaimer #2: I will post this also on the Nano ...
cdna direct rna nanopore sequencing written 13 days ago by Macspider3.0k
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Comment: C: ETE3 TreeError: 'Nodes are not connected!': how to fix?
... The same way you would except any other error in python, nothing fancy. ...
written 4 weeks ago by Macspider3.0k
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Comment: C: Converting MUMmer snps file to a real VCF file
... Yes, please read through this github issue that I closed some weeks ago, I believe it's the same issue :) https://github.com/MatteoSchiavinato/Utilities/issues/1 (to improve readability, could you wrap the code parts of your answer inside a code block?) ...
written 8 weeks ago by Macspider3.0k
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Comment: C: Extract allele read counts for heterozygous positions in VCF
... Yes, I am afraid so. If this information is not stored during the pileup, it won't be possible to extract it from a VCF file. ...
written 9 months ago by Macspider3.0k
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Answer: A: Extract allele read counts for heterozygous positions in VCF
... When you do the pileup, for example with samtools, you can require additional tags to be present in your `INFO` and `GENOTYPE`. These are specified via the `-t` option. I usually ask for: −t DP,AD,ADF,ADR,DP4 Note that DP4 is deprecated but still present in the output if you require it. It con ...
written 9 months ago by Macspider3.0k
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Comment: C: Trimmomatic; How to get only q20 < q < q30 reads
... Have as much as you need within programs that you can re-run at any time, save all logs possible. This is really 90% of the efficiency, imho! Everytime something like this happens, you be like changing your script parameters and re-run it. Even if it took a lot to get where you are, re-running it wo ...
written 9 months ago by Macspider3.0k
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Comment: C: Trimmomatic; How to get only q20 < q < q30 reads
... I work routinely with FASTQ files that are > 500GB and I would repeat the whole analysis ^^ putting every command into a script doesn't take so long, after all, if they execute one after the other. ...
written 9 months ago by Macspider3.0k
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Comment: C: cutoff for expressed genes in DESeq2
... This might be the best suggestion you'll ever receive about it. ...
written 9 months ago by Macspider3.0k

Latest awards to Macspider

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Popular Question 8 months ago, created a question with more than 1,000 views. For Insert size selection for RNASeq data: does it make sense?
Scholar 9 months ago, created an answer that has been accepted. For A: How to convert .bed file to .juncs file using Tophat?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Scholar 9 months ago, created an answer that has been accepted. For A: How to convert .bed file to .juncs file using Tophat?
Popular Question 10 months ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Popular Question 11 months ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Popular Question 11 months ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Scholar 11 months ago, created an answer that has been accepted. For A: How to convert .bed file to .juncs file using Tophat?
Popular Question 13 months ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
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Scholar 21 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'

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