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Devon Ryan
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dare_devil
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Recent Replies
Comment: Adjust Y axis scale in ggplot2
by
santiagoboccardo31
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0
Thank you! I will give a try to your suggestion :D
Comment: Strategy for designing small gene panel from large scale transcriptomic experime
by
ATpoint
60k
Can you describe the experimental setup and question a bit more? it is unclear to me what you are trying to do and achieve.
Answer: How to make a read count matrix from multiple bed files generated by ROSE
by
Rory Stark
★
1.5k
I'm not 100% sure what the specific issue is here?
You can do a differential binding analysis (default `DESeq2`by default) very easily:
…
Answer: Detect Structural varirant from VCF file
by
Pierre Lindenbaum
144k
If your ambiguous question is about finding SV from a VCF file of small variants/SNVs, you can try `bcftools roh` https://samtools.github.i…
Comment: Detect Structural varirant from VCF file
by
brunobsouzaa
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720
To search for structural variants you can use, for example, Manta or Pindel... Of course, there's a lot of other tools for that. To campare…
Comment: Count number of times a value appear in correlation matrix
by
Basti
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320
I think you should explain your "Fisher transformation", which code did you use ?
Answer: Detect Structural varirant from VCF file
by
dthorbur
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160
Your question is unclear - what pipelines/tools were used to generate these SV VCFs and why wouldn't you trust them?
There are dozens o…
Comment: can i take promoter upstream 2kb from tss ?
by
dthorbur
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160
Just a quick update since I was looking for *D. melanogaster* core promoters today, I came across the Eukaryotic Promoter Database which ha…
Answer: split vcf by individual
by
kitobo6683
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0
To split large VCF files into smaller parts is a bit tricky task because with the manual process there are chances of data loss and the pro…
Comment: Extract the mRNA sequences of all the orthologs of a eukaryotic gene
by
manaswwm
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250
If I understand your question correctly - you have a reference gene (mRNA sequence) and you want to perform alignments of this gene across …
Comment: Count number of times a value appear in correlation matrix
by
ali
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0
`cor.matrix` was generated by the function `cor(t(data))` where data has genes as rows and samples as columns. And below is the output of s…
Comment: gatk error: reference file does not exist
by
parinv
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40
thank you. This helped in solving the error.
Comment: Normalization of RNASeq counts with a reference gene (/genes)
by
fracarb8
▴
760
The scaling step is used because in Oncoland your have multiple datasets, and you want to be able to compare them together. By scaling, you…
Answer: downloading human rRNA.fasta
by
ATpoint
60k
https://www.gencodegenes.org/human/
Take the `Transcript sequence` fasta file and extract whatever you need. You could `grep` for `rRNA`…
Comment: How to count mapping rates for ChIP-seq?
by
Ian
5.8k
Hello. What did you use to map the reads? I use Bowtie2, the log file of which gives useful information.
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