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A: What Are The Most Common Stupid Mistakes In Bioinformatics?
A: What Are The Most Common Stupid Mistakes In Bioinformatics?
A: What Are The Most Common Stupid Mistakes In Bioinformatics?
A: What Are The Most Common Stupid Mistakes In Bioinformatics?
Comment: Where to find the homopolymer regions bed file for Hg002 genome?
Visualization of PROKKA Annotation Result?
A: snakemake output directory
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Recent Replies
Comment: Where to find the homopolymer regions bed file for Hg002 genome?
by
Pierre Lindenbaum
161k
cross-posted https://bioinformatics.stackexchange.com/questions/22401
Comment: Tumour purity and ploidy estimation
by
bp22
▴ 60
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…
Comment: Ensembl gene id conversion
by
ATpoint
81k
Can you add some examples. It is hard to debug textual descriptions.
Answer: Which experiments generate Position Frequency Matrix?
by
ATpoint
81k
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
by
ATpoint
81k
> 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…
Comment: Can I compare kallisto counts from samples with different amount of reads?
by
ATpoint
81k
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…
Comment: Error in edgeR/Deseq2 Analysis
by
ATpoint
81k
Please ask at https://help.galaxyproject.org/ which is the Galaxy help forum.
Comment: RNAseq 1 control 2 different treatment
by
matteo.levorato
• 0
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…
Comment: snakemake output directory
by
进
• 0
it is right answer
Comment: I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calcul
by
Spring
• 0
Thank you for the kind guidance!
Answer: I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calcul
by
ATpoint
81k
No, you either have the spliced and unspliced counts available that you need, or you need the fastq files to generate them. Before you dive…
Comment: Convert GVF to VCF
by
george-hall-ucl
• 0
This has moved - it is now at: [https://github.com/Ensembl/ensembl-variation/blob/main/scripts/misc/release/gvf2vcf.pl][1]. [1]: https:…
Comment: I'm new to cell ranger. Can single cells prepared with a protocol other than the
by
Spring
• 0
Thank you very much!
Comment: I'm new to cell ranger. Can single cells prepared with a protocol other than the
by
Spring
• 0
Thank you so much! If the 10x Chromium protocol is not used, should the processing be done with HISAT2, FeatureCounts, and so on?
Comment: I'm new to cell ranger. Can single cells prepared with a protocol other than the
by
fracarb8
★ 1.6k
For the paper, they used the `indrop` pipeline (https://github.com/indrops/indrops), and you should have a look at it, and try to run with …
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