Tutorial:
Sequence Alignment from Scratch with BWA
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Comment: boxplot issue
by
ATpoint
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Please get used to make your question reproducible and precise, meaning provide example data and reduce code to a minimum.
Answer: Total No of Genes of GENCODE Release 43
by
ATpoint
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As I said, I assume that you are doing something on old/overwritten variables or a wrong GTF. This is how it is:
a<-rtracklayer::i…
Answer: Any tips in landing a bioinformatic job?
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Vincent Laufer
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Do you have a public facing github page (or equivalent) that provides examples of bioinformatics workflows you've created?
For myself, if …
Comment: Align miRNA library (small RNA-seq) without trimming
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Paola
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Hi Ming
Untrimmed reads have 76bp in average.
Answer: Align miRNA library (small RNA-seq) without trimming
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Ming Tommy Tang
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bowtie 1 is good for short read < 50bp, how long is your read? bowtie2 is better for reads > 50 bp
Comment: Differences in RNAseq Variant Calling and Allele Specific Expression
by
afei
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Hi!
I'm also confused by this. And the site (https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum) is closed. Have you …
Comment: Variant caller reports a homozygous variant genotype, but more reads are associa
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rebeliscu
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Indeed, I thought the quality might be a factor. Still, given the information, it seems odd to me that that call was made.
Thanks for you…
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
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cfos4698
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To generate a VCF file one would normally pipe the input of an `mpileup` command into an actual `call` command. For example:
```
bcftools …
Answer: PTM-aware protein folding / docking
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Mensur Dlakic
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Your assumption is correct - AlphaFold pTM has nothing to do with post-translational modifications. See [**here**][1].
Not to discourage…
Answer: Admixture cv error
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Declan
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I had this issue today and was able to resolve it by changing the random seed Admixture uses by adding `-s time` (which sets the random see…
Comment: Total No of Genes of GENCODE Release 43
by
ahmad
•
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The following is the correct code
gtf_43<-rtracklayer::import('gencode.v43.primary_assembly.annotation.gtf')
dtgtf_43<-data.frame(gtf_4…
Comment: Total No of Genes of GENCODE Release 43
by
ahmad
•
0
Hello,
thanks for replying, by mistake I paste the wrong code. the following is the corrected
gtf_43<-rtracklayer::import('gencode.v43…
Comment: Kallisto bustools for scRNA-seq
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dsull
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I have no idea what that is besides a bunch of jumbled sequences. You'll need look up the structure of the reads / library from wherever yo…
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First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
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There is some somatic SV study on these HCC1395: https://doi.org/10.1186/s13059-022-02816-6.
There is also a CNA preprint from years ago b…
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