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Showing top results for tag: Transcript • reset
5
votes
3
replies
662
views
Why Are Transcripts Differentially Expressed but Not Genes in RNA-seq Analysis? — Confusion Around Transcript-Level Differential Expression
Gene Transcript Count RSEM
10 days ago by Cooper • 0
0
votes
4
replies
308
views
The definition of a gene
gene lncrna transcript
10 days ago by zizigolu ★ 4.3k
0
votes
3
replies
296
views
GTF merging with gffcompare
gtf merging annotation RNA-Long reads transcript
updated 12 days ago by 8.9k • written 14 days ago by • 0
6
votes
14
replies
710
views
Choosing the best representative transcript for a gene
transcript
16 days ago by Biodee • 0
0
votes
3
replies
448
views
Script for Rstudio
Rstudio Transcript kallisto analysis
updated 8 weeks ago by ★ 6.9k • written 8 weeks ago by • 0
8
votes
7
replies
4.0k
views
Ensembl Api: How To Print All Transcript Isoforms As A Multifasta Alignment
ensembl transcript isoform multiple fasta
updated 3 months ago by ★ 3.9k • written 13.5 years ago by ★ 5.1k
0
votes
0
replies
222
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript Quantify non-coding
5 months ago by Varsha • 0
7
votes
7
replies
825
views
Longest transcript variant per gene
transcript longest variant orthofinder
5 months ago by sansan96 ▴ 130
1
vote
1
reply
699
views
adding gene and CDS feature types in ensemble gtf annotation with transcript and exon features
GTF GFF transcript CDS exon
updated 6 months ago by ★ 1.1k • written 6 months ago by ▴ 20
0
votes
5
replies
723
views
How do I get utr transcript coordinates?
UTR transcript
8 months ago by Salvatore • 0
3
votes
5
replies
730
views
Functional domain data from NM_ transcript id
transcript functional-domain
updated 9 months ago by 44k • written 9 months ago by • 0
3
votes
4
replies
638
views
Transcript Based Annotation of Variants Using Annovar
Annovar SNV Transcript Variant
updated 9 months ago by ★ 3.0k • written 9 months ago by ▴ 180
0
votes
0
replies
741
views
Transcript Assembly for Multiple Species Using StringTie and Orthogroup Discovery using OrthoFinder
Species StringTie Orthogroups Transcript Assembly
10 months ago by dtnondorf • 0
1
vote
1
reply
443
views
Transcript count normalization using Deseq2
transcript DESeq2
updated 12 months ago by 85k • written 12 months ago by ▴ 20
2
votes
2
replies
645
views
Ensembl transcript IDs
Ensembl transcript IDs
written 12 months ago by ▴ 50
15
votes
6
replies
2.1k
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome bed transcript TSS
13 months ago by Rafael Soler ★ 1.3k
1
vote
1
reply
461
views
transcript abundance, control and wgs
transcript tumour
updated 16 months ago by ★ 1.2k • written 16 months ago by ▴ 50
3
votes
1
reply
840
views
Annotate CDS and UTR given transcript
annotation GFF GFFCompare CDS transcript
18 months ago by gtho123 ▴ 260
0
votes
1
reply
555
views
Error in change Affymetrix transcript cluster id to Gene Symbol in microarray
microarray id cluster Affymetrix transcript
updated 18 months ago by 146k • written 18 months ago by ▴ 10
2
votes
2
replies
762
views
Remove multiple gene id from bed file
transcript bed genes
updated 17 months ago by 44k • written 18 months ago by • 0
1
vote
2
replies
801
views
Is third-generation sequencing/long-read-sequencing the only way to identify the full length sequence of a novel transcript?
long-read-sequencing third-generation-sequencing transcript
18 months ago by wangziwei0010 ▴ 30
4
votes
5
replies
1.4k
views
How to generate GFF/GTF file from cDNA transcipts FASTA file?
gff3 gtf transcript cDNA
18 months ago by BioinfoBee • 0
2
votes
1
reply
934
views
Transcript variants conversion from Ensembl ENST to NM
Ensembl transcript RefSeq
updated 19 months ago by ★ 2.4k • written 20 months ago by • 0
15
votes
21
replies
3.7k
views
6 follow
Aberrant splicing in bulk RNAseq
aberrant-splicing transcript isoform exon
updated 17 months ago by • 0 • written 20 months ago by ▴ 190
0
votes
0
replies
369
views
RefSeq predicted transcripts/proteins alterations compared to genomic sequence
protein genomics annotation transcript refeq
21 months ago by bram_danneels • 0
1
vote
1
reply
977
views
Is a "transcript annotation" different from a "genome annotation?"
Transcript Annotation Genome RNA-Seq
updated 22 months ago by 24k • written 22 months ago by • 0
0
votes
4
replies
923
views
SRA: realistic data from reference transcript
reference SRA transcript
2.0 years ago by shinyjj ▴ 50
7
votes
9
replies
1.6k
views
Tools to check the length of isoforms in reference transcript
transcript histogram isoform
2.0 years ago by shinyjj ▴ 50
0
votes
2
replies
412
views
Transcript Abundances Meta-transcriptome
Transcript Meta-transcriptome Abundances RNA-Seq
written 2.0 years ago by ▴ 60
0
votes
0
replies
519
views
Download Isoform expression data from tcga
cancer transcript gene isoform
2.0 years ago by nourmahfel • 0
1
vote
2
replies
714
views
MaSuRCA for Transcript Assembly
rnaseq transcriptome masurca genome transcript
2.1 years ago by kilcdincer ▴ 10
0
votes
3
replies
765
views
Determining transcripts for repetitive elements in RNA-seq data
transcript rna-seq stringtie
updated 2.1 years ago by 13k • written 2.1 years ago by ▴ 250
1
vote
2
replies
778
views
RefSeq Transcript vs Reference Genome sequence
Transcript RefSeq
updated 2.1 years ago by ▴ 930 • written 2.1 years ago by ▴ 50
0
votes
0
replies
576
views
confusion about gffread extracting transcript sequence based on stringtie merge gtf
gene stringtie ID gffread transcript
2.1 years ago by liyong ▴ 80
1
vote
2
replies
888
views
empty output of cds.fa from gffread
seq extract cds gffread transcript
2.1 years ago by liyong ▴ 80
0
votes
3
replies
837
views
why appears transcritps with 0 expression if it was used for the novo transcriptome assembly?
estimation abundance kallisto assemby Trynity transcript transcriptome
2.2 years ago by Pilar • 0
4
votes
3
replies
1.1k
views
Mapping GeneSymbol plus cDNA position to a Chr:Position ... without transcript ID.
annotation splice site transcript build
2.2 years ago by LauferVA 4.5k
3
votes
9
replies
1.8k
views
Extract nucleotide sequence from a RefSeq Transcript ID
nucleotide refseq transcript sequence entrez
2.2 years ago by LauferVA 4.5k
4
votes
7
replies
2.7k
views
About normalization of the datasets from Harmonized TCGA data
protein transcript normalisation
updated 9 months ago by 44k • written 2.3 years ago by ▴ 10
0
votes
2
replies
696
views
Identifying and quantifying transcript variants in RNA-seq data
rnaseq nf-core variant RNA-seq transcript
2.3 years ago by MieszkoL ▴ 10
0
votes
2
replies
808
views
Get nucleotide sequence of assembled RNA transcripts
transcript assembly RNA-seq chimeric RNA
updated 2.3 years ago by ▴ 430 • written 2.4 years ago by ▴ 20
5
votes
7
replies
2.5k
views
6 follow
Kallisto and Salmon give different results
transcript expression salmon hisat2 kallisto
updated 2.5 years ago by ★ 6.9k • written 2.5 years ago by ▴ 30
2
votes
5
replies
2.8k
views
Extract transcript fasta sequences using gtf
transcript using fasta gtf sequences
updated 2.5 years ago by 13k • written 2.5 years ago by ▴ 30
1
vote
1
reply
639
views
Are analagous Ensembl and RefSeq transcript sequences identical?
transcript refeq annotation ensembl
updated 2.5 years ago by 146k • written 2.5 years ago by ▴ 10
4
votes
12
replies
2.7k
views
Retrieving gene ID using transcripts ID from Entrez database using CLI or Batch Entrez
database ID gene transcript Entrez
2.6 years ago by hans ▴ 20
1
vote
1
reply
577
views
Mapping gene coordinates to transcript exons
genes transcript positions exon
updated 2.7 years ago by 3.3k • written 2.7 years ago by ▴ 180
0
votes
2
replies
965
views
Differential transcript usage from Salmon data
DTU rnaseqDTU transcript differential stageR
updated 22 months ago by ▴ 140 • written 2.7 years ago by ▴ 260
11
votes
12
replies
2.1k
views
7 follow
What do we call a transcript?
RNAseq mRNA CentralDogma Transcript Splicing
updated 2.7 years ago by 15k • written 2.7 years ago by ▴ 80
3
votes
2
replies
833
views
Identifying common genes which show different transcript and protein expression
expression transcript differential R protein
2.7 years ago by vin23 ▴ 10
2
votes
2
replies
813
views
AlphaFold to Ensembl transcript mapping
Ensembl AlphaFold transcript mapping
updated 2.7 years ago by ▴ 120 • written 2.7 years ago by • 0
50 results • Page 1 of 1
Recent Votes
The Biostar Herald for Friday, November 01, 2024
The Biostar Herald for Friday, November 01, 2024
Clustering and dynamic tree cutting
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
Answer: Coverage data for TCGA BAM files
Answer: Coverage data for TCGA BAM files
RNA-Seq vs DNA-Seq variant calling
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Recent Replies
Comment: Are there any preferred trajectory/pseudotime analyses that do not require an ar by Jean-Karim Heriche 27k
Maybe consider seriation/ordination as an alternative.
Comment: dedup STAR transcriptome file using umi_tools by i.sudbery 20k
There are bulk protocols that include UMIs. Lexogen's CORRAL kits for example. Or NEB's NEBNext UMI adaptors.
Answer: dedup STAR transcriptome file using umi_tools by Michael 55k
I am quite sure that you cannot use UMI_tools to deduplicate bulk RNA-seq. The different oligo adapter sequences on each bead introduce UMI…
Answer: dedup STAR transcriptome file using umi_tools by i.sudbery 20k
I don't know if any reason you shouldn't be able to index the bam produced by STAR, although you will need to sort them first.
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by wangziwei0010 ▴ 30
Hi ATpoint, Thank you for your though provoking answer. Big fans! Actually I have some normal cells in each sample, and I found good mixt…
Answer: Differential binding analysis between different TFs by Ming Tommy Tang ★ 4.5k
have you taken a look at csaw? https://bioconductor.org/books/release/csawBook/ also, I am not sure how you can compare different TFs, the…
Comment: R encountering fatal error and quitting the session by Dunois ★ 2.7k
Have you tried running this in a fresh, clean `R` session with no other (unnecessary) packages and data being loaded into memory? How much …
Comment: PyDeseq2 - InvalidIndexError by Dunois ★ 2.7k
You most likely have duplicates somewhere in there in the column that is currently serving as index to (I am guessing) the counts DataFrmae…
Comment: What to do with sequences without hits after doing blast against a reference tra by Dunois ★ 2.7k
Expand your search by searching these (two) sequences against other sets of sequences. That said, why does it feel like this is an [XY pro…
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
It's confounded. SCtransform is not doing anything in such situations and hatmony operates on a per-cell embeddings level and not per gene …
Comment: count number of polymorphic sites among samples in vcf by vaellis • 0
I'm wondering if this could work: `bcftools query -f '[%GT]\n' my.vcf.gz | awk '{ gsub(/\./, ""); print }' | grep -Ev '^(.)\1+$' | wc -l` …
Comment: GISTIC 2.0 parameter change not happening by Ram 44k
You should contact the [GenePattern google group](https://groups.google.com/g/genepattern-help) - that's where you stand a higher chance of…
Comment: find marker using scRNAseq data by allingt • 0
What method are you using to identify markers and does it allow for nested designs?
Comment: count number of polymorphic sites among samples in vcf by vaellis • 0
I will look into this. Thank you!
Comment: count number of polymorphic sites among samples in vcf by vaellis • 0
example vcf: ``` CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ind1 ind2 ind3 ind4 chr1 100 . C …
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