User: Macspider

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Macspider2.2k
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Vienna - BOKU
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macspider_music
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2 days ago
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1 year, 3 months ago
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Posts by Macspider

<prev • 476 results • page 1 of 48 • next >
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Answer: A: Gene Prediction Softwares
... What I used: https://www.blast2go.com/ But simply searching in google scholar will give you tons of papers where people did this in different ways. You can also homebrew it yourself, building blast databases and blasting sequences against them. ...
written 2 days ago by Macspider2.2k
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Comment: C: Phytophthora spp genome comparison
... I guess it depends on what you want to assess, of the gene content. Distribution? Function? Abundance of different families? ...
written 2 days ago by Macspider2.2k
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Comment: C: Unable to blast entire coding sequence of gene
... This should be marked as answer! ...
written 2 days ago by Macspider2.2k
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Comment: C: Error in extracting Counts from the bam file using htseq-count
... `-s`: are your data "reverse"? What happens when you use "no", or "yes"? `-t`: maybe you should provide the right feature type? `-r`: is the order by name or by position? ...
written 6 days ago by Macspider2.2k
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Comment: C: Error in extracting Counts from the bam file using htseq-count
... So if for: - sample.sorted.bam - gencode.v27.primary_assembly.annotation.gtf you check the path, the file is there? This is the cause of 90% of the issues, regardless of the experience of the researcher. ...
written 6 days ago by Macspider2.2k
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Comment: C: Error in extracting Counts from the bam file using htseq-count
... No, you definitely didn't do anything wrong in the alignment. The problem is arising because the command line interpreter is not parsing correctly the BAM and the GFF argument that you provide. Sorry to ask but, is that the FULL command that you ran? Or did you rewrite it to show it to us? Also, w ...
written 6 days ago by Macspider2.2k
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Comment: C: Are 2 replicates per sample sufficient for RNA-seq data analysis?
... The million dollar question! Two are definitely not enough, but sometimes we have to deal with it and use only those. Three are usually considered a good number, but statistically speaking you'd need 20-30 ^^ ...
written 6 days ago by Macspider2.2k
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Comment: C: error in differential analysis using splAdder
... This is a python error, whenever you get an `IndexError` in such a situation it usually means that your file is not formatted as it should. How is a line of your file structured? Are all of them like that? ...
written 6 days ago by Macspider2.2k
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Comment: C: Differential gene expression from RNAseq data. Before or after annotation?
... @DanGaston definitely my point too, what I wrote was a pseudocode to show that the logic behind it is not that hard. I usually accept multimapping reads and then select the primary alignment for each read. For two equally good alignments (i.e. same score) many mapping programs like the tuxedo-suite ...
written 7 days ago by Macspider2.2k
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Comment: C: Genome DNA sequence pattern matching
... I meant that you can use any mapping program you find to do this. It's not the name of a program. ...
written 7 days ago by Macspider2.2k

Latest awards to Macspider

Appreciated 16 days ago, created a post with more than 5 votes. For Best way to compare two samples in a VCF file
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 27 days ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 5 weeks ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 5 weeks ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 9 weeks ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 10 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 Remove duplicates from reads: best practices?
Appreciated 3 months ago, created a post with more than 5 votes. For Best way to compare two samples in a VCF file
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: 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'
Popular Question 6 months ago, created a question with more than 1,000 views. For Best way to compare two samples in a VCF file
Student 9 months ago, asked a question with at least 3 up-votes. For DESeq2 proper design setting
Scholar 9 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
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Scholar 9 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
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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'
Scholar 10 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 10 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'

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