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Showing top results for tag: RNA-Seq • reset
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43
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Omics data collection and merging of datasets from different studies
analysis RNA-seq omics data transcriptomics
5 hours ago by BioQueen • 0
2
votes
2
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87
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bioinformatics pipelines on GCP or AWS
RNA-seq google ChIP-seq cloud
updated 19 hours ago by 33k • written 19 hours ago by ★ 1.1k
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0
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82
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Job: BIOINFORMATICIAN II
RNA-seq Genomics Job Transcriptomics
21 hours ago by lianov ▴ 10
3
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2
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90
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Input source for the IPA tool
IPA RNA-seq
21 hours ago by Mozart ▴ 280
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2
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105
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rna seq batch effects and cross species study
RNA-Seq effects different datasets batch
updated 22 hours ago by 11k • written 1 day ago by ▴ 20
3
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4
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200
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Whole genome sequencing and RNA sequencing data analysis for a bacterial strain
RNA-Seq Gene Whole genome sequencing
17 hours ago by pbaranw • 0
2
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2
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184
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EM algorithm in Kallisto
RNA-seq Kallisto
2 days ago by Mozart ▴ 280
2
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2
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178
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Correct way to make multiple comparisons on DESeq2?
expression differential DESeq DESeq2 RNA-seq
2 days ago by jbnrodriguez ▴ 30
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2
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113
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Highly mapped to introns
distribution read RSeQC RNA-seq exon intron
updated 2 days ago by 5.8k • written 3 days ago by • 0
2
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2
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112
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FFPE and fresh-frozen samples in different RNA seq batches?
batch RNA-seq fresh-frozen FFPE
2 days ago by Axel • 0
2
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2
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96
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Batch correction for DE analysis
DEGs MDSplot batchcorrection RNA-seq mRNA
updated 3 days ago by 53k • written 3 days ago by ▴ 10
3
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2
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104
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Genome indexing with hisat2 and samtools
samtools index Hisat2 RNA-seq genome
updated 3 days ago by 106k • written 3 days ago by ▴ 20
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0
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49
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Segemehl -D option doesnt work for allowing differences
alignment RNA-Seq segemehl
updated 4 days ago by 34k • written 4 days ago by ▴ 50
3
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14
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749
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DGE from tumor-adjacent normal pair RNA-seq data. For an individual, no replicate
RNA-seq DGE statistics tumor-normal
2 days ago by field654 ▴ 20
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0
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46
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Trouble running Cyclum for my scRNA-seq analysis
cell Cyclum scRNA-seq RNA-seq cycle
4 days ago by 23jinny • 0
3
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3
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1.6k
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Find Information about TCGA samples from GDC data portal
RNA-Seq TCGA GDC Sample information
updated 7 days ago by ▴ 10 • written 3.3 years ago by ▴ 70
3
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9
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550
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Filter DGElist object: keep only genes expressed in sample at the same time as a particular gene of interest
edger RNA-seq dgelist R
8 days ago by Ondina ▴ 10
0
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6
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267
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Transcripts mapping using Salmon
Salmon mRNA-seq RNA-seq total
10 days ago by g.wang2 ▴ 10
1
vote
1
reply
136
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Download TCGA and GTEX data from Xena toilHub for (full genome but for 1 cancer/tissue type)
GTEX UCSCXenaTools TCGA RNA-seq Xena
updated 10 days ago by ★ 2.3k • written 12 days ago by • 0
1
vote
2
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176
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Can the Non strand specify RNAseq data annotate genome?
RNA-Seq
10 days ago by yiren • 0
3
votes
5
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348
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Commandline BLAST - errors?
line BLAST RNA-seq command
updated 8 days ago by ★ 1.0k • written 11 days ago by • 0
1
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3
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487
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Differential expression analysis between normal/cancer on recount2 data
recount GTEX TCGA RNA-seq batch
updated 10 days ago by 77k • written 12 days ago by • 0
3
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5
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1.3k
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which matrix should NMF use in single cell RNA seq data to find diferential gene program?
RNA-Seq
updated 13 days ago by ▴ 30 • written 17 months ago by ▴ 10
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1
reply
241
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TCGAbiolinks: which normalization before differential expression analysis (legacy=TRUE vs. legacy=FALSE)
TCGAbiolinks limma TCGA RNA-seq normalization
updated 14 days ago by ▴ 290 • written 14 days ago by • 0
1
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3
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355
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scRNAseq - infer type of single-cell chemistry from fastq
scRNA-seq single cell RNA-Seq
updated 14 days ago by • 0 • written 7 months ago by ★ 1.7k
2
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4
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1.0k
views
List of human protein coding genes with given name (known function?)
RNA-Seq Annotation Human
updated 15 days ago by ★ 8.8k • written 2.1 years ago by ★ 2.5k
0
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2
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154
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Interpreting read coverage over gene body plot
chipster rseqc illumina rna-seq
14 days ago by Mikael • 0
1
vote
6
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285
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Input of 173 genes into enrichGO but no pathways are shown
clusterProfiler RNA-seq enrichGO R
updated 16 days ago by 53k • written 16 days ago by • 0
0
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1
reply
310
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How long running FEELnc_codpot.pl step takes? (FEELnc long-non coding RNAs)
RNA-Seq
updated 16 days ago by • 0 • written 11 months ago by ▴ 30
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0
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80
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Forum: Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR
RNA-Seq microarray qRT-PCR
17 days ago by Antonio R. Franco ★ 4.7k
0
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1
reply
313
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Duplicates in ICGC expression data
RNA-Seq ICGC
updated 18 days ago by • 0 • written 12 months ago by ▴ 50
3
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4
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275
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Bad volcano plot
diferential-gene-expression rna-seq sc-rnaseq
updated 16 days ago by ▴ 100 • written 18 days ago by ★ 1.3k
14
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25
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16k
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12 follow
htseq-counts output merge into one matrix ??
rna-seq bioinformatics gene expression counts
updated 20 days ago by ▴ 350 • written 6.9 years ago by ▴ 130
2
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7
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562
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Survival analysis for several genes
R RNA-Seq
updated 20 days ago by 106k • written 7 months ago by ▴ 10
2
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4
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2.5k
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How can I use R to do many genes survival analysis at the same time?
R TCGA survival RNA-Seq
updated 13 days ago by • 0 • written 3.2 years ago by ▴ 10
3
votes
1
reply
288
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Change location of 'fragments' in multiome Seurat file
RNA-Seq R Seurat Signac ATAC-Seq
21 days ago by V ▴ 320
0
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1
reply
157
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Ranking gene list for GOrilla gene ontology enrichment analysis
enrichment GOrilla rna-seq ontology GO
updated 21 days ago by ▴ 190 • written 21 days ago by • 0
3
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9
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1.5k
views
Which counts to use for RNA-seq heatmap and PCA?
RNA-seq heatmap EdgeR PCA
updated 22 days ago by 53k • written 21 months ago by ▴ 80
1
vote
1
reply
119
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featureCounts: unable to find chromosome in SAM header
featureCounts count RNA-seq table
updated 22 days ago by ★ 3.3k • written 22 days ago by • 0
0
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1
reply
133
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Approach to building regression models or classifiers with high number of parameters but small sample size
cancer machine-learning R scRNA-seq RNA-seq
updated 22 days ago by ★ 13k • written 22 days ago by ▴ 10
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0
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62
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Error in Robust Rank Aggregation
next-gen RNA-Seq sequencing R
22 days ago by ashwing.kofficial ▴ 10
4
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2
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170
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Transcriptional noise detection and Salmon TPMs
salmon isoforms tximport rna-seq tpms
17 days ago by karlaarz • 0
0
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0
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100
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Strategies to learn about a gene of interest from single-cell RNA-seq data
scRNA-seq RNA-seq single-cell
24 days ago by randalljellis ▴ 90
0
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1
reply
106
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htseq-count returns : does not contain a 'gene' attribute
htseq-count RNA-Seq
24 days ago by ziziqolo ▴ 10
1
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2
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163
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Tutorials for Robust Rank Agrregation
RNA-Seq R sequencing next-gen
24 days ago by ashwing.kofficial ▴ 10
6
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10
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2.5k
views
DESeq2 with a small number of genes
DESeq2 SARTools RNA-Seq Count-normalisation
updated 25 days ago by ▴ 40 • written 4.9 years ago by ▴ 630
4
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5
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419
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Calculate fold change in edgeR with one sample per condition
R edgeR expression rna-seq differential
24 days ago by mohammedtoufiq91 ▴ 110
8
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6
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685
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How to convert log2 scale RNA-Seq expression data to linear scale data
expression edgeR R rna-seq fold-change
updated 27 days ago by 5.8k • written 28 days ago by ▴ 110
1
vote
5
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606
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how to combine either Rna-seq datasets or results from analysis of Rna-seq datasets to get a visual result
RNA-Seq sequencing next-gen
25 days ago by ashwing.kofficial ▴ 10
0
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2
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243
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When importing my quant.sf files into R using tximport, should I set 'ignoreTxVersion' to True or False?
Salmon RNA-Seq tximport R
updated 26 days ago by ▴ 150 • written 26 days ago by • 0
50 results • Page 1 of 1
Recent Votes
Comment: How to remove Illumina TruSeq Index adapters reverse (R2 reads )
How can I draw this plot?
Interpreting output of BCFtools RoH
Answer: Is there any software that can use ATAC-seq to identify super enhancer
A: Alignment and mapping
Comment: Flat Volcano plot
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
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Teacher to Philipp Bayer 7.3k
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Recent Replies
Comment: get read length from sra by Renesh ★ 2.0k
The suggested methods works. Here is another method using the [SRA toolkit][1] fastq-dump -X 1 -Z SRR5790106 | sed -n '2p' | awk '{ pr…
Comment: Primers trimming from Illumina paired-end reads by BBDuk software by GenoMax 106k
Following should work. Give it a try and let me know. bbduk.sh -Xmx2g in1=test_R1.fq in2=test_R2.fq out1=R1_trim.fq out2=R2_trim.fq li…
Answer: Database for Enhancers with Coordinates by Papyrus ★ 1.3k
Also check [EnhancerAtlas][1], apart from coordinates it provides predictions for enhancer-gene target interactions, which may be useful. …
Comment: How can I draw this plot? by gubrins ▴ 90
Heys, did you manage to plot it?
Comment: get read length from sra by GenoMax 106k
You will only get average length of reads (which may or may not be very useful) using [Entrezdirect][1]. $ esearch -db sra -query "SRR…
Comment: Interpreting output of BCFtools RoH by gubrins ▴ 90
Heys, did you manage in interpreting and visualizing the output? I'm in the same situation...
Comment: which tool can I use to detect CNVs? by brunobsouzaa ▴ 560
`cnvkit` and `ExomeDepth` are great tools for that. Also, both are pretty straightforward to use.
Comment: rsem-calculate-expression with STAR takes forever but without error by Fleur • 0
Thanks both! I will try :) :)
Comment: rsem-calculate-expression with STAR takes forever but without error by Fleur • 0
Ah yes, sounds similar to tmux which is what I'm using. That also makes sure that the job keeps running when you close the terminal. Thanks…
Comment: which tool can I use to detect CNVs? by patelk26 ▴ 250
You could try CNVkit. You can create a reference copy number profile without normal samples.
Answer: Is there any software that can use ATAC-seq to identify super enhancer by jared.andrews07 ★ 11k
The original paper actually used a collection of TFs + Mediator. ROSE was not designed for H3K27ac use, though both the authors and others …
Comment: get read length from sra by ATpoint 53k
https://www.biostars.org/p/115936/#115962
Comment: script to organize files by Galileo • 0
I found a solution: used dos2unix on the files that have '$'\r' at the end :)
Comment: How to remove Illumina TruSeq Index adapters reverse (R2 reads ) by Info.shi ▴ 10
Thank you so much for quick response if I understand you well is it I need to specify maximum base pair of adapter to trim. And I was wou…
Comment: script to organize files by Galileo • 0
Thanks jv, this seems to work but read added '$'\r' at the end of filenames of the second column and thus mv cannot find the file. Any idea…
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