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Recent Replies
Comment: Why does assigning genes with biomart give me different values than using a tran
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GenoMax
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According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
Answer: RNAseq RNA content
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noodle
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There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2]
and then run [multiqc][3…
Comment: Where to get the following bed file?
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wyuan37
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Hi, I emailed them and did get the bed file! Thank you so much.
Answer: Post-imputation QC for input into GWAS analyses
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LauferVA
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1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data
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You can simply ignore read 2. It is not adding any information since your small RNA's are going to be small and were completely sequenced b…
Comment: Overlapping Ranges within Granges object
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ntsopoul
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does this work with a single .bed file?
Comment: Finding variants within a subset of a BAM file
by
ramiro.barrantes
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Actually, I found a solution in downloading "bam slices" from TCGA ([https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/][1]) , which …
Comment: Overlapping Ranges within Granges object
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ntsopoul
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![enter image description here][1]Here is some representative data and an image in igv of one gene. I have loaded the .bed file in igv. As …
Answer: RNAseq RNA content
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ntsopoul
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I guess he/she means raw RNA. Roughly 2% of all RNA is mRNA the rest is rRNA. I think the first thing you need to figure out is with which …
Comment: Overlapping Ranges within Granges object
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ATpoint
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I would probably collapse overlapping regions with `reduce` to create the second GRanges. Can you add some representative data? Using dput?
Comment: Overlapping Ranges within Granges object
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ntsopoul
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I have one Granges object and not two. Every IRanges entry is the critical region of the gRNA. Can this still work?
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by
J.
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FYI if you also have this problem, this seems to be a pretty good solution: https://github.com/harvardinformatics/degenotate
Comment: Biomart issue, why so few 3'utrs?
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GenoMax
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AFAIK "MANE" project is only for human protein-coding genes.
One potential explanation. Out of the 2000 ID's only 125 may be MANE.
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