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Recent Replies
Comment: Why does assigning genes with biomart give me different values than using a tran
by
GenoMax
142k
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
by
noodle
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580
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?
by
wyuan37
•
0
Hi, I emailed them and did get the bed file! Thank you so much.
Answer: Post-imputation QC for input into GWAS analyses
by
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
by
GenoMax
142k
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
by
ntsopoul
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60
does this work with a single .bed file?
Comment: Finding variants within a subset of a BAM file
by
ramiro.barrantes
•
0
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
by
ntsopoul
▴
60
![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
by
ntsopoul
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60
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
by
ATpoint
82k
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
by
ntsopoul
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60
I have one Granges object and not two. Every IRanges entry is the critical region of the gRNA. Can this still work?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
by
J.
▴
40
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?
by
GenoMax
142k
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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