User: tiago211287

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tiago2112871.1k
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Posts by tiago211287

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Comment: C: how to extract the genomic positions and chromosome number for a list of genes
... 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 3 months ago by tiago2112871.1k
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Comment: C: how to extract the genomic positions and chromosome number for a list of genes
... Can you please share a sample of the remaining id's? ...
written 4 months ago by tiago2112871.1k
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Comment: C: how to extract the genomic positions and chromosome number for a list of genes
... 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 4 months ago by tiago2112871.1k
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Answer: A: how to extract the genomic positions and chromosome number for a list of genes
... 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 4 months ago by tiago2112871.1k
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Comment: C: Bioinformatics question regarding multilevel pie chart
... Maybe Adobe Illustrator? ...
written 4 months ago by tiago2112871.1k
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Comment: C: Deconvolve bulk expression data into individual immune components.
... Maybe Helpful? https://www.nature.com/articles/s41467-018-08023-x ...
written 4 months ago by tiago2112871.1k
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Comment: C: ATAC-seq DE analysis
... Your link does not work anymore. Could you update it? Thanks! ...
written 7 months ago by tiago2112871.1k
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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 11 months ago by tiago2112871.1k
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Comment: C: Filtering rRNA from RNAseq data
... You can normally align the reads against genome + annotation (gencode), using STAR for example which can count the number of reads/feature. Then just check the annotated rRNA gene count percentage. You would need "good" samples as a control of what is normal/bad. ...
written 12 months ago by tiago2112871.1k
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Comment: C: want to pick up the strongest peaks in all the duplicates
... Have you already called your peaks? You can Use MACS2 for peak calling. To only then, choose strong peak signals. I would also use deeptools to access Chip-Seq Sequencing quality and statistics. ...
written 12 months ago by tiago2112871.1k

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