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3
votes
7
replies
1.7k
views
Is removing rRNAs, tRNAs, etc really a necessary step in the miRNA analysis?
mirdeep2 miRNA RNA-seq
updated 15 months ago by ▴ 30 • written 3.0 years ago by ▴ 170
5
votes
4
replies
2.7k
views
How to subset the output of tximport in DE analysis using DEseq2
DEseq2 tximport rna-seq r
updated 2.3 years ago by 82k • written 3.9 years ago by ▴ 170
2
votes
12
replies
5.6k
views
How to get KEGG pathway names in KEGG enrichment analysis using clusterprofiler
annotation enrichment KEGG clusterprofiler RNA-Seq
updated 2.7 years ago by ★ 2.6k • written 4.0 years ago by ▴ 170
0
votes
0
replies
442
views
how to annotate mapping peaks within a defined genomic region？
piRNA genome RNA-seq annotation
2.9 years ago by tianshenbio ▴ 170
0
votes
4
replies
890
views
How to merge genomic features shared by more than one samples
bedtools gene RNA-seq bed annotation
3.0 years ago by tianshenbio ▴ 170
0
votes
1
reply
1.1k
views
Convert a DNA sequence to MEME format
FIMO fasta motif MEME-suite format conversion
updated 3.1 years ago by 141k • written 3.1 years ago by ▴ 170
8
votes
6
replies
1.9k
views
How to select genes with multi-exon 3'UTR
rna-seq genome gff gene
updated 3.1 years ago by 8.5k • written 3.1 years ago by ▴ 170
1
vote
0
replies
2.8k
views
Functional annotation(GO,KEGG): Blast2GO+KAAS or EggNOG
blast2go eggnog kegg rna-seq genome
updated 3.2 years ago by 20 • written 4.0 years ago by ▴ 170
2
votes
8
replies
3.4k
views
Why sortmerna 4.2.0 runs so slow?
RNA-Seq sortmerna software error RNA rna-seq
updated 3.2 years ago by ▴ 20 • written 4.0 years ago by ▴ 170
2
votes
3
replies
4.3k
views
How to get a list of all KEGG ko terms vs names?
kegg annotation rna-seq
updated 2.6 years ago by ▴ 10 • written 4.0 years ago by ▴ 170
8
votes
12
replies
16k
views
6 follow
Clusterprofiler error: No gene can be mapped
RNA-seq GO enrichment R GO clusterProfiler
updated 3.0 years ago by ▴ 20 • written 4.1 years ago by ▴ 170
3
votes
4
replies
965
views
RNA-seq raw data lost
RNA-Seq next-gen sequencing sequence
updated 3.5 years ago by 141k • written 3.5 years ago by ▴ 170
4
votes
2
replies
2.2k
views
What would be the best strategy to merge the GO annotation from blast2go, InterProScan, and eggnog
interproscan eggnog blast2go GO RNA-Seq
updated 3.7 years ago by 20 • written 3.9 years ago by ▴ 170
2
votes
4
replies
754
views
Can I directly blast mRNAs against nr database or I need to convert it to cds first
rna-seq annotation blast genome
updated 3.7 years ago by 13k • written 3.7 years ago by ▴ 170
3
votes
4
replies
3.7k
views
How to visualise KEGG pathway?
kegg enrichment RNA-Seq
updated 3.7 years ago by ▴ 430 • written 3.8 years ago by ▴ 170
0
votes
3
replies
3.5k
views
How do I remove certain sequences in fast based on header?
RNA-Seq sequence fasta
updated 3.8 years ago by ▴ 380 • written 3.8 years ago by ▴ 170
1
vote
2
replies
1.3k
views
Blast: use best hit or top20 hits?
blast blast2go GO annotation RNA-Seq
3.9 years ago by tianshenbio ▴ 170
0
votes
0
replies
818
views
How to specify -s option in RNAhybrid to predict miRNA targets?
miRNA rna-seq sequence RNAhybrid
3.9 years ago by tianshenbio ▴ 170
0
votes
3
replies
1.2k
views
Compare expression level of isoforms among conditions - TPM or deseq2 normalised counts?
RNA-Seq deseq2 tximport salmon
3.9 years ago by tianshenbio ▴ 170
0
votes
4
replies
2.5k
views
Correct gtf file format (AGAT toolkit)
RNA-Seq gff gtf AGAT gff3
updated 3.9 years ago by 8.5k • written 3.9 years ago by ▴ 170
10
votes
5
replies
3.6k
views
Is Stringtie a suitable tool for both gene and transcript quantification?
stringtie RNA-Seq sequencing featurecounts gene
updated 22 months ago by • 0 • written 3.9 years ago by ▴ 170
1
vote
3
replies
2.2k
views
Read counts at gene and transcript level - hisat2+Featurecounts or Stringtie?+deseq2
RNA-Seq featurecounts stringtie hisat2 deseq2
3.9 years ago by tianshenbio ▴ 170
2
votes
2
replies
630
views
Proper design in deseq2
RNA-Seq deseq2 gene R
updated 3.9 years ago by 14k • written 3.9 years ago by ▴ 170
1
vote
1
reply
3.4k
views
Filter out DE genes with low counts in deseq2
RNA-Seq R gene deseq2
updated 3.9 years ago by 82k • written 3.9 years ago by ▴ 170
0
votes
2
replies
1.6k
views
Gffread_How to obtain fasta files of gene features (ORF, UTR) by transcripts based on gff?
RNA-Seq Assembly genome sequence gene
3.9 years ago by tianshenbio ▴ 170
4
votes
3
replies
1.6k
views
How to extract sequence of a specific feature in gff
rna-seq gff genome assembly
updated 3.9 years ago by 8.5k • written 3.9 years ago by ▴ 170
4
votes
2
replies
1.7k
views
After read mapping, count exons or genes?
RNA-Seq featurecounts genome
updated 3.9 years ago by 82k • written 3.9 years ago by ▴ 170
0
votes
5
replies
778
views
Many paralogous genes in GO enrichment results
RNA-Seq GO enrichment gene
3.9 years ago by tianshenbio ▴ 170
0
votes
2
replies
2.4k
views
How to generate a dataframe of deseq2 result excluding 'low counts' and 'outliers' ?
deseq2 RNA-Seq
updated 3.9 years ago by 87k • written 3.9 years ago by ▴ 170
6
votes
4
replies
3.8k
views
What to choose as background genes in GO enrichment analysis
RNA-Seq go enrichment goseq clusterprofiler
updated 3.9 years ago by ★ 2.9k • written 3.9 years ago by ▴ 170
2
votes
4
replies
1.7k
views
Too many enriched GO terms using Goseq
goseq RNA-Seq enrichment GO
3.9 years ago by tianshenbio ▴ 170
9
votes
4
replies
9.2k
views
How to combine multiple pheatmap figures and use common legend?
R pheatmap ggarrange gridarrange
updated 22 months ago by ▴ 10 • written 4.0 years ago by ▴ 170
1
vote
4
replies
1.3k
views
BLAST Database creation error: is not a valid local ID
blast RNA-Seq database software error alignment
4.0 years ago by tianshenbio ▴ 170
3
votes
7
replies
1.1k
views
How to interpret different results in deseq2 due to different design
RNA-Seq R sequencing deseq2
4.0 years ago by tianshenbio ▴ 170
4
votes
6
replies
1.8k
views
Is transcriptome assembly a necessary step in RNA-seq?
RNA-Seq Assembly genome sequencing alignment
updated 4.0 years ago by 100k • written 4.0 years ago by ▴ 170
3
votes
9
replies
1.1k
views
Reformat my txt file
RNA-Seq gene ontology
4.1 years ago by tianshenbio ▴ 170
3
votes
7
replies
2.7k
views
How to extract 3'UTR regions
RNA-Seq genome 3'UTR Assembly
updated 4.2 years ago by 15k • written 4.2 years ago by ▴ 170
4
votes
2
replies
925
views
Blastn: no output after local alignment
blast RNA-Seq RNA miRNA mirbase
updated 4.2 years ago by ★ 27k • written 4.2 years ago by ▴ 170
0
votes
5
replies
1.3k
views
Forward and reverse files with different number of lines after sortmeRNA
RNA-Seq sortmerna
updated 4.3 years ago by 141k • written 4.3 years ago by ▴ 170
0
votes
12
replies
2.0k
views
run multiple files for sortmeRNA
RNA-Seq rna-seq sortmerna sequencing
4.3 years ago by tianshenbio ▴ 170
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