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Bogdan
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pavelasquezv
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Recent Replies
Answer: Extract data from Signac RegionMatrix?
by
Chironex
▴
40
object@assays$ATAC@positionEnrichment$my_region_matrix
and also
object@assays$ATAC@positionEnrichment$my_region_matrix$condit…
Comment: Any tips in landing a bioinformatic job?
by
ATpoint
70k
Great answer, narrowing it down the the key points!
Comment: How to remove unknown batch-batch effects from GEO datasets
by
ATpoint
70k
The righthand plot might be totally fine once you remove that one outlier on the left, try that first. The batch effect manifesting along P…
Comment: using CITE-seq data to cluster single cells
by
ATpoint
70k
If it is really just two genes then why not just plotting logcounts of gene1 vs logcounts of gene2 as in a FACS scatter plot and see whethe…
Comment: How to remove unknown batch-batch effects from GEO datasets
by
2317711200
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0
As a beginner, I hope to receive professional answers. If necessary, I can provide rewards and R code.
Answer: Align miRNA library (small RNA-seq) without trimming
by
ATpoint
70k
For miRNA you should trim the data to the actual expected miRNA length (20-something bp, I would need to look up the exact value). Reason i…
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
★
2.6k
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…
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