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How to get information about antisense/sense lncRNAs?
RNA-Seq lncrna gencode
updated 3.2 years ago by ★ 16k • written 3.2 years ago by ▴ 120
2
votes
7
replies
2.4k
views
How to get the phastcons score for protein coding genes and lncRNAs?
RNA-Seq phastcons genome conservation
updated 3.4 years ago by 20 • written 4.1 years ago by ▴ 120
0
votes
3
replies
1.5k
views
How to get transcript ID and tpm from the gtf files of ballgown outputs?
RNA-Seq ballgown hisat2 gtf awk
updated 3.4 years ago by 43k • written 3.4 years ago by ▴ 120
3
votes
5
replies
2.2k
views
How to get the output on multiple files into one file in sbatch script?
RNA-Seq strand rseqc sbtach slurm
updated 3.4 years ago by 20 • written 3.6 years ago by ▴ 120
1
vote
1
reply
1.3k
views
Problem with bedtools intersect with two gtfs
RNA-Seq gtf bedtools intersect
3.5 years ago by newbie ▴ 120
7
votes
11
replies
4.0k
views
Differential analysis show different results with edgeR and in box plot with t-test
RNA-Seq R differential analysis edger boxplot
updated 3.5 years ago by • 0 • written 5.0 years ago by ▴ 120
6
votes
5
replies
1.8k
views
Is it good to merge transcripts tpm to gene which is of different gene type?
RNA-Seq kallisto tpm
updated 3.5 years ago by • 0 • written 3.5 years ago by ▴ 120
0
votes
4
replies
2.7k
views
Why counts to tpm gives different values compared to tpm from kallisto?
RNA-Seq tpm kallisto rawcounts featureCounts
3.5 years ago by newbie ▴ 120
0
votes
4
replies
2.3k
views
Interpretation of two PCA plots
RNA-Seq pca clustering
updated 3.5 years ago by 14k • written 3.5 years ago by ▴ 120
2
votes
9
replies
2.8k
views
Why there are low assigned reads in featureCounts output and different outputs for quality checks?
RNA-Seq featureCounts alignment qualimap reads
updated 3.6 years ago by 13k • written 3.6 years ago by ▴ 120
1
vote
5
replies
1.7k
views
Warnings in the Hisat2 alignment output files
RNA-Seq hisat2 cutadapt alignment
updated 3.6 years ago by 14k • written 3.6 years ago by ▴ 120
0
votes
2
replies
1.9k
views
Why sequence length disturbution failed after adapter trimming: fastqc?
RNA-Seq fastqc qualitycontrol adaptertrimming
updated 3.7 years ago by ▴ 330 • written 3.7 years ago by ▴ 120
1
vote
1
reply
1.4k
views
Denovo assembly or Reference based assembly for identifying novel lncRNAs
RNA-Seq stringtie hisat2 denovoassembly lncrna
3.7 years ago by newbie ▴ 120
3
votes
3
replies
758
views
correlation between expression and tumor size
R expression tumorsize correlation
updated 3.7 years ago by 87k • written 3.7 years ago by ▴ 120
0
votes
1
reply
1.2k
views
How to check whether mutation in a gene activating or inactivating other genes?
mutation maftools wgs activation
updated 3.7 years ago by 13k • written 3.7 years ago by ▴ 120
0
votes
9
replies
2.6k
views
Error with Rseqc infer_experiment - unknown datatype
RNA-Seq rseqc inferexperiment gtf2bed
3.7 years ago by newbie ▴ 120
4
votes
10
replies
1.1k
views
How to look for a specific nucleotides of lncRNA sequence in TCGA data?
RNA-Seq sequence alignment blat tcga
updated 3.8 years ago by 87k • written 3.8 years ago by ▴ 120
0
votes
1
reply
1.2k
views
How to make a Pathway enrichment Heatmap with padjusted values?
RNA-Seq r pathways heatmap
updated 3.8 years ago by 13k • written 3.8 years ago by ▴ 120
0
votes
3
replies
1.1k
views
Problem in subsetting a gtf based on ids in another file
gtf slurm grep shell bash
3.8 years ago by newbie ▴ 120
0
votes
3
replies
1.3k
views
Questions about detecting module related to which Group using WGCNA?
RNA-Seq R wgcna coexpression trait
updated 3.9 years ago by 87k • written 3.9 years ago by ▴ 120
2
votes
5
replies
1.1k
views
How to detect cis and trans protein coding genes of interested lncRNAs?
RNA-Seq ChIP-Seq lncrna wgcna
updated 3.9 years ago by 19k • written 3.9 years ago by ▴ 120
4
votes
3
replies
1.8k
views
Differential analysis heatmap without hclust
RNA-Seq heatmap complexheatmap r hclust
updated 4.0 years ago by ▴ 30 • written 4.9 years ago by ▴ 120
3
votes
9
replies
14k
views
How to create a GSEA enrichment plot for the phenotypes in R?
RNA-Seq r gsea lncrna
updated 4.0 years ago by ★ 1.3k • written 4.0 years ago by ▴ 120
4
votes
10
replies
1.3k
views
How to check the pattern in a specific file present in which other files in a directory?
linux grep find xargs
updated 4.0 years ago by 161k • written 4.0 years ago by ▴ 120
1
vote
3
replies
2.6k
views
How to create a network of multiple clusters in co-expression network?
RNA-Seq wgcna network coexpression mrna
updated 4.0 years ago by ▴ 680 • written 4.0 years ago by ▴ 120
0
votes
0
replies
942
views
bedtools usage to extract the non overlaps between two gtfs
gtf bedtools intersect mitranscriptome lncrna
4.1 years ago by newbie ▴ 120
3
votes
3
replies
1.3k
views
How to check the mutual exclusiveness between two genes?
mutation mutual exclusivity statistics
updated 4.2 years ago by 5.7k • written 4.2 years ago by ▴ 120
30
votes
13
replies
11k
views
8 follow
How to get read counts on transcript level using featurecounts?
RNA-Seq featurecounts geneexpression
updated 4.2 years ago by ★ 7.1k • written 4.2 years ago by ▴ 120
3
votes
4
replies
1.0k
views
Question about processed microarray data from ArrayExpress
microarray geneexpression r RNA-Seq arrayexpress
updated 4.2 years ago by 82k • written 4.2 years ago by ▴ 120
0
votes
5
replies
2.8k
views
feature selection using random forest
RNA-Seq R randomforest featureselection
updated 4.2 years ago by ★ 6.0k • written 4.2 years ago by ▴ 120
5
votes
14
replies
2.2k
views
How to make a heatmap showing signatures of scores from 0 to 1 in R?
RNA-Seq heatmap complexheatmap r signatures
4.8 years ago by newbie ▴ 120
4
votes
9
replies
2.4k
views
soft threshold for co-expression analysis using WGCNA based on scale independence
RNA-Seq R wgcna co-expression
4.9 years ago by newbie ▴ 120
5
votes
5
replies
2.9k
views
what to do when differential analysis heatmap looks like this?
RNA-Seq R heatmap differentialanalysis edger
updated 4.9 years ago by ▴ 10 • written 5.0 years ago by ▴ 120
0
votes
13
replies
1.9k
views
Differential analysis using cell-line data with replicate information
RNA-Seq r edger celllines differentialanalysis
5.0 years ago by newbie ▴ 120
7
votes
1
reply
5.0k
views
How to filter low expressed genes based on TPM expression?
RNA-Seq r tpm gene filtering
updated 5.0 years ago by ★ 2.2k • written 5.0 years ago by ▴ 120
4
votes
5
replies
1.3k
views
How to compare samples between two different platforms?
RNA-Seq R correlation microarray
5.2 years ago by newbie ▴ 120
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