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Tutorial:
Sequence Alignment from Scratch with BWA
alignment
bwa
DNA
54 minutes ago by
barslmn
★ 1.4k
1
vote
3
replies
422
views
Tutorial:
Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo
DNA
motif
gibbssampling
splice
52 minutes ago by
barslmn
★ 1.4k
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Any tips in landing a bioinformatic job?
Answer: Any tips in landing a bioinformatic job?
Answer: Any tips in landing a bioinformatic job?
Answer: Any tips in landing a bioinformatic job?
Answer: What is the NCBI's definition of an "atypical genome"?
Answer: Variant caller reports a homozygous variant genotype, but more reads are associa
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
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Comment: boxplot issue
by
ATpoint
70k
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
70k
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?
by
Vincent Laufer
★ 2.5k
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
by
Paola
▴ 10
Hi Ming Untrimmed reads have 76bp in average.
Answer: Align miRNA library (small RNA-seq) without trimming
by
Ming Tommy Tang
★ 2.9k
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
• 0
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
by
rebeliscu
▴ 50
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
by
cfos4698
▴ 730
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
by
Mensur Dlakic
★ 23k
Your assumption is correct - AlphaFold pTM has nothing to do with post-translational modifications. See [**here**][1]. Not to discourage…
Answer: Admixture cv error
by
Declan
• 0
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
• 0
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
by
dsull
★ 4.0k
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…
Comment: Aberrant splicing in bulk RNAseq
by
dsull
★ 4.0k
First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
Comment: Using Copy Number Alterations detected in other studies for the same tumor cell
by
lethalfang
▴ 90
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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