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Forum: Site Use Guidelines
meta biostars Guidelines
updated 20 days ago by 43k • written 14.6 years ago by 100k
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Forum: Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career advice
updated 29 days ago by ★ 2.5k • written 29 days ago by • 0
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Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
12 days ago by Estevão ▴ 10
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Forum: VCF bulk handling
bcftools SnpEff WGS VEP VCF
27 days ago by Javier • 0
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Forum: Bioinformatics: Where do I start
Sequencing
updated 28 days ago by 43k • written 28 days ago by ▴ 20
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Forum: Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation scRNA llm
21 days ago by yxwucq • 0
6 results • Page 1 of 1
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Comment: sci-RNA-seq
The Biostar Herald for Monday, May 13, 2024
Answer: Finding variants within a subset of a BAM file
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Help with IGV abbreviation
Split multiallelic SNPs to biallelic from vcf
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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.
Comment: Where to get the following bed file? by wyuan37 • 0
Thanks! Super helpful.
Answer: Post-imputation QC for input into GWAS analyses by LauferVA 4.2k
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 ▴ 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 ▴ 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: RNAseq RNA content by ATpoint 82k
What is "row RNA"?
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 ▴ 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. https:…
Answer: Biomart issue, why so few 3'utrs? by i.sudbery 19k
The MANE-select transcripts are pairs of identically annotated transcripts in ReqSeq and Ensembl. The 3' UTR is the region where otherwise …
Comment: sci-RNA-seq by ATpoint 82k
Please understand that this impossibly can be answered without any code or plots, or details in general. "Hey my car does not start, it mak…
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