User: tiago211287
tiago211287 • 1.2k
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Posts by tiago211287
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... Why can't you just use your bed file with your alignment files (BAMs) by using featureCounts software to count the number of fragments in each peak region? ...
written 26 days ago by
tiago211287 • 1.2k
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Comment:
C: enhanced volcano plot
... You can use Samtools to figure out the command used by the facility to generate the bam file. Look at the @PG tag might see the genome/annotation file names which might give you a clue of the reference used for alignment.
> samtools view -H file.bam
You generated a Count matrix and then what? W ...
written 26 days ago by
tiago211287 • 1.2k
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... You can try to convert your retired IDs using the [ID Conversion tool][1] for GRCh37. Or maybe this [Biostar][2] link can help you to access the GRCh37 using biomaRt.
This Ensembl [page][3] contains information about converting between both assemblies.
[1]: http://grch37.ensembl.org/Homo_sapien ...
written 17 months ago by
tiago211287 • 1.2k
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... Can you please share a sample of the remaining id's?
...
written 17 months ago by
tiago211287 • 1.2k
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... You need a column with your regular gene_id_versions called **ensembl_gene_id_version**. And Another column with the edited **ensembl_gene_id** without versions. created with gsub.
my_ids$ensembl_gene_id <- gsub("\\..*","", my_ids$ensembl_gene_id_version)
Only then you can merge, using:
...
written 17 months ago by
tiago211287 • 1.2k
2
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... The numbers after the dot are the gene version. It might be that you have very old gene versions.
You may try to use R to get your information. Removing the Ensembl gene version.
Like this:
#Get gene names annotation
source("http://bioconductor.org/biocLite.R")
BiocInstaller::biocLite ...
written 17 months ago by
tiago211287 • 1.2k
3
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1
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1
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... Maybe Adobe Illustrator? ...
written 17 months ago by
tiago211287 • 1.2k
0
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101
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... Maybe Helpful?
https://www.nature.com/articles/s41467-018-08023-x ...
written 17 months ago by
tiago211287 • 1.2k
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3
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Comment:
C: ATAC-seq DE analysis
... Your link does not work anymore. Could you update it? Thanks! ...
written 21 months ago by
tiago211287 • 1.2k
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Comment:
C: bam file merge
... In http://www.htslib.org/doc/samtools-1.2.html,
it says,
> -h is specified the @SQ headers of input files will be merged into
> the specified header, otherwise they will be merged into a composite
> header created from the input headers. If in the process of merging
> @SQ lines for coor ...
written 2.1 years ago by
tiago211287 • 1.2k
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