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Recent Replies
Comment: add INFO tag to vcf with bcftools
by
Javier
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0
Hi, im traying to do something similar, could you share the code to do what you describe.
Thanks
Comment: Visualization of PROKKA Annotation Result?
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Joe
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Colin's answer is essentially the right one I believe, but the more immediate consideration is: *what are you actually trying to show?*
Mo…
Comment: Bioinformatics_where do i start
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Pierre Lindenbaum
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https://www.biostars.org/p/9554614/ ; https://www.biostars.org/p/98983 ; https://www.biostars.org/p/9583727/ :https://www.biostars.org/p/4…
Answer: Bwa sampe - BGI
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Pierre Lindenbaum
161k
bwa sampe produces unsorted SAM , not BAM.
converting SAM to BAM will reduce the size
sorting the BAM will reduce the size (you can …
Comment: Where to find the homopolymer regions bed file for Hg002 genome?
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Bikram Kumar
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0
Hi! Should I delete the stack exchange post? I didn't know that cross posting is bad.
[https://meta.stackoverflow.com/a/425789/5140632][1]
…
Answer: Visualization of PROKKA Annotation Result?
by
colindaven
6.3k
You need a genome browser and you can probably use GBK or gff3 format.
Here are some suggestions - I like JBrowse best, Artemis in its …
Comment: Where to find the homopolymer regions bed file for Hg002 genome?
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Pierre Lindenbaum
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cross-posted https://bioinformatics.stackexchange.com/questions/22401
Comment: Tumour purity and ploidy estimation
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bp22
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Hi Llyod98,
This issue is still unresolved and I have not been able to find a tool or solution for purity and ploidy estimation when ther…
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ATpoint
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Can you add some examples. It is hard to debug textual descriptions.
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ATpoint
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Yes, ChIP-seq or similar methods that assay the DNA binding of a protein. But for a reliable matrix you don't need one or two but many data…
Comment: Statistical Advice Needed for RNAseq Data Analysis
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ATpoint
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> ensuring it's not merely a product of random chance
If your approach of getting DEGs is a proper and sound one (e.g. DESeq2 or limma) th…
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Unequal numbers of reads are normal, that is why normalization is needed. If you want to do simple analysis such as number of detected gene…
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ATpoint
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Please ask at https://help.galaxyproject.org/ which is the Galaxy help forum.
Comment: RNAseq 1 control 2 different treatment
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matteo.levorato
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yes, this is what I did. However, since my treatments are very similar each other, when I check upregulated genes in one treatment, they ar…
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