User: Macspider

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Macspider2.8k
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Vienna - BOKU
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macspider_music
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Posts by Macspider

<prev • 540 results • page 1 of 54 • next >
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Comment: C: How to annotate FASTA genome using GFF genes from another genome?
... Already done, but thanks. ...
written 2 days ago by Macspider2.8k
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Comment: C: How to annotate FASTA genome using GFF genes from another genome?
... Might consider this. I'm working with *E. coli* so... then perhaps I can use RATT with that! ...
written 2 days ago by Macspider2.8k
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Comment: C: How to annotate FASTA genome using GFF genes from another genome?
... Thanks, I'll give them a try! ...
written 2 days ago by Macspider2.8k
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Comment: C: How to annotate FASTA genome using GFF genes from another genome?
... > I tried RATT but couldn't really use it (needs ENSEMBL IDs). I can't use RATT sadly. @genomax I don't necessarily trust the original annotation, I just want to give it a try if there is a simple way to transfer it, before doing my own gene prediction which is more time-consuming. ...
written 2 days ago by Macspider2.8k
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How to annotate FASTA genome using GFF genes from another genome?
... I have a FASTA genome sequence of a particular accession of a species that I'm using. It was also annotated (in terms of genes and CDS) by unknown people some unknown time ago. This genome has shown to have issues and therefore I have re-assembled it into a new genome. Of course I could run a gene p ...
fasta annotation gff program genome written 3 days ago by Macspider2.8k
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Comment: C: RepeatModeler - FastaDB error
... Did you solve it? And how? I'm having the same issue. ...
written 6 weeks ago by Macspider2.8k
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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 4 months 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 months ago by Macspider2.8k
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Comment: C: Bowtie2 mapped just 50% of the reads
... Is your library stranded? ...
written 5 months 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 5 months ago by Macspider2.8k

Latest awards to Macspider

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Great Question 4 months ago, created a question with more than 5,000 views. For Remove duplicates from reads: best practices?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Scholar 5 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: How to add tophat and bowtie to the path?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 7 months ago, created a question with more than 1,000 views. For DESeq2 proper design setting
Appreciated 7 months ago, created a post with more than 5 votes. For A: Explanation of a Perl script
Great Question 7 months ago, created a question with more than 5,000 views. For Best way to compare two samples in a VCF file
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: How to add tophat and bowtie to the path?
Scholar 9 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 12 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Good Question 12 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 13 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
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 17 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Appreciated 17 months ago, created a post with more than 5 votes. For Best way to compare two samples in a VCF file
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 17 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 18 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 18 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 19 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'

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