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Answer: Add samples IDs to Seurat object when integrating different samples to do differ
Add samples IDs to Seurat object when integrating different samples to do differential expression analysis
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Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
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Comment: genome finishing
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I may be wrong here so someone feel free to correct me, but I've never noticed a variants file from `SPAdes`, and certainly never used one …
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You will need to obtain the software from an official source. I believe Perseus is a paid-for program and as such sharing via the forum wou…
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Joe
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This post does not fit the theme of this forum.
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
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Istvan Albert
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this is not bioinformatics and is not a tool and as such it is off-topic on this site
Comment: calculating genomic coverage/ base overlap in R
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Sayantani
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# Install and load necessary packages if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") …
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
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GenoMax
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Instead of simply posting a chunk of code it would be useful to add a line or two to say where this could would be useful. Not immediately …
Comment: Duplicated reads (IDs) from nanopore sequencing
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GenoMax
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Thanks for the link. We never use "pod5_fail" folders when re-basecalling so we did not see this issue. Current version of MinKNOW now make…
Answer: calculating genomic coverage/ base overlap in R
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marco.barr
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with `findOverlaps` function in `GenomicRanges` package or directly with this package `GeneOverlap`. Check out the documentation of these …
Comment: Annotating file using bcftools
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Pierre Lindenbaum
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> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Answer: Annotating file using bcftools
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Pierre Lindenbaum
161k
I think your're annotating $REF/All_20180423.vcf.gz (DBSNP isn't it ? = no genotype) with your vcf as the database ro_imputed_hrcgrch37.R2_…
Comment: Duplicated reads (IDs) from nanopore sequencing
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marco.barr
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I had the same problem in this iusse [https://github.com/nanoporetech/dorado/issues/603][1] and I solved it as they say here [1]: https…
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ATpoint
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Looking at this briefly, it is small sample size and you do not correct for any potential confounders. Use PCA or MDS to explore the data. …
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GenoMax
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> It is confirmed (and solved in another thread) that we have significant overlapping paired end reads. Can you provide a reference to sai…
Comment: Duplicated reads (IDs) from nanopore sequencing
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GenoMax
142k
> I get the exact same read with the same ID and all more than once If you have short(er) reads you could be seeing secondary alignments. …
Answer: Duplicated reads (IDs) from nanopore sequencing
by
marco.barr
▴ 110
Hi, I'm also working with ONT data and with dorado. From experience I tell you that some versions of MInKNOW have bad management of fast5 f…
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