Moderator: WouterDeCoster
WouterDeCoster ♦ 35k
- Reputation:
- 35,390
- Status:
- Trusted
- Location:
- Belgium
- Website:
- https://gigabaseorgiga...
- Twitter:
- wouter_decoster
- Last seen:
- 5 hours ago
- Joined:
- 2 years, 10 months ago
- Email:
- d*************@gmail.com
I am a research associate at the Center for Molecular Neurology, University of Antwerp & VIB, focussing on analysis of sequencing data with the aim of identifying variants relevant to neurodegenerative diseases, and mainly structural variants using long read PromethION sequencing.
Posts by WouterDeCoster
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... The term you are looking for is a "hybrid assembly". Using that for googling will give you plenty of hits. ...
written 8 hours ago by
WouterDeCoster ♦ 35k
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C: What is RPKM/FPKM > 1 or 3 or 5?
... Yes. You filter the obtained RPKM counts to only keep genes with expression above that cut-off. ...
written 16 hours ago by
WouterDeCoster ♦ 35k
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C: What is RPKM/FPKM > 1 or 3 or 5?
... Those which have their RPKM/FPKM above a certain threshold are considered "expressed". ...
written 16 hours ago by
WouterDeCoster ♦ 35k
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C: What is RPKM/FPKM > 1 or 3 or 5?
... See for example this blog post: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/ ...
written 17 hours ago by
WouterDeCoster ♦ 35k
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... I converted your post to a "Question" (because that's what it is) and shortened the title to make it more concise. ...
written 17 hours ago by
WouterDeCoster ♦ 35k
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... > I want to merge two platforms to have 3700 genes together.
Probably important to state what the aim of your downstream analysis is. ...
written 18 hours ago by
WouterDeCoster ♦ 35k
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... https://www.biostars.org/p/309884/ ...
written 20 hours ago by
WouterDeCoster ♦ 35k
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C: How to merge several FPKM files?
... Both cufflinks and FPKM are NOT recommended anymore. What is the aim of your analysis? ...
written 20 hours ago by
WouterDeCoster ♦ 35k
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Comment:
C: AfterQC what is the reason killed
... > 250 gb SSD but as i know Afterqc needs just 4 gb
You are confusing RAM with hard disk.
Your error message is incomplete. ...
written 20 hours ago by
WouterDeCoster ♦ 35k
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Comment:
C: for loop over bwa aln
... Put an echo in your loop to see how it looks like:
for i in $(cat READ1_list | sed s'/\-READ1.fastq.gz//' | sort)
do
echo "bwa sampe reference/reference.unaligned.fasta $i\-READ1.sai $i\-READ2.sai $i\-READ1.fastq.gz $i\-READ2.fastq.gz \
| samtools view -bS - > $i\-pe.bam"
...
written 20 hours ago by
WouterDeCoster ♦ 35k
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For C: Plot number of mutations in each cancer type in VCF files?
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For A: mapping of rna seq read to reference seq
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For C: Plot number of mutations in each cancer type in VCF files?
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For Interesting bioinformatics blogs (2017 edition)
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For A: mapping of rna seq read to reference seq
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For A: The order of part processions of RNA-Seq data
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