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5
votes
4
replies
1.6k
views
How to subset the output of tximport in DE analysis using DEseq2
DEseq2 tximport rna-seq r
updated 7 months ago by 64k • written 2.2 years ago by ▴ 130
1
vote
12
replies
3.3k
views
How to get KEGG pathway names in KEGG enrichment analysis using clusterprofiler
annotation enrichment KEGG clusterprofiler RNA-Seq
updated 12 months ago by ★ 2.5k • written 2.3 years ago by ▴ 130
0
votes
0
replies
240
views
how to annotate mapping peaks within a defined genomic region？
piRNA genome RNA-seq annotation
14 months ago by tianshenbio ▴ 130
0
votes
0
replies
568
views
Comment: Comment: How to merge genomic features shared by more than one samples
15 months ago by tianshenbio ▴ 130
0
votes
0
replies
345
views
Is removing rRNAs, tRNAs, etc really a necessary step in the miRNA analysis?
miRNA mirdeep2 gene RNA-seq RNA
15 months ago by tianshenbio ▴ 130
0
votes
1
reply
568
views
Comment: Comment: How to merge genomic features shared by more than one samples
15 months ago by tianshenbio ▴ 130
0
votes
4
replies
568
views
How to merge genomic features shared by more than one samples
bedtools gene RNA-seq bed annotation
15 months ago by tianshenbio ▴ 130
0
votes
1
reply
680
views
Convert a DNA sequence to MEME format
FIMO fasta motif MEME-suite format conversion
updated 16 months ago by 119k • written 16 months ago by ▴ 130
1
vote
0
replies
1.3k
views
Comment: Comment: How to select genes with multi-exon 3'UTR
16 months ago by tianshenbio ▴ 130
8
votes
6
replies
1.3k
views
How to select genes with multi-exon 3'UTR
rna-seq genome gff gene
updated 16 months ago by 7.2k • written 16 months ago by ▴ 130
1
vote
0
replies
1.8k
views
Functional annotation(GO,KEGG): Blast2GO+KAAS or EggNOG
blast2go eggnog kegg rna-seq genome
updated 17 months ago by 20 • written 2.3 years ago by ▴ 130
0
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1
reply
2.2k
views
Comment: C: Why sortmerna 4.2.0 runs so slow?
18 months ago by tianshenbio ▴ 130
2
votes
8
replies
2.2k
views
Why sortmerna 4.2.0 runs so slow?
RNA-Seq sortmerna software error RNA rna-seq
updated 18 months ago by ▴ 20 • written 2.3 years ago by ▴ 130
2
votes
3
replies
2.1k
views
How to get a list of all KEGG ko terms vs names?
kegg annotation rna-seq
updated 10 months ago by ▴ 10 • written 2.3 years ago by ▴ 130
8
votes
12
replies
7.2k
views
6 follow
Clusterprofiler error: No gene can be mapped
RNA-seq GO enrichment R GO clusterProfiler
updated 15 months ago by ▴ 20 • written 2.4 years ago by ▴ 130
0
votes
0
replies
495
views
Comment: C: RNA-seq raw data lost
21 months ago by tianshenbio ▴ 130
3
votes
4
replies
495
views
RNA-seq raw data lost
RNA-Seq next-gen sequencing sequence
updated 21 months ago by 119k • written 21 months ago by ▴ 130
4
votes
2
replies
1.5k
views
What would be the best strategy to merge the GO annotation from blast2go, InterProScan, and eggnog
interproscan eggnog blast2go GO RNA-Seq
updated 24 months ago by 20 • written 2.2 years ago by ▴ 130
0
votes
0
replies
517
views
Comment: C: Can I directly blast mRNAs against nr database or I need to convert it to cds fi
2.0 years ago by tianshenbio ▴ 130
0
votes
0
replies
517
views
Comment: C: Can I directly blast mRNAs against nr database or I need to convert it to cds fi
2.0 years ago by tianshenbio ▴ 130
2
votes
4
replies
517
views
Can I directly blast mRNAs against nr database or I need to convert it to cds first
rna-seq annotation blast genome
updated 2.0 years ago by 13k • written 2.0 years ago by ▴ 130
3
votes
4
replies
2.0k
views
How to visualise KEGG pathway?
kegg enrichment RNA-Seq
updated 2.0 years ago by ▴ 430 • written 2.1 years ago by ▴ 130
0
votes
3
replies
1.4k
views
How do I remove certain sequences in fast based on header?
RNA-Seq sequence fasta
updated 2.1 years ago by ▴ 360 • written 2.1 years ago by ▴ 130
0
votes
0
replies
2.0k
views
Comment: C: How to visualise KEGG pathway?
2.1 years ago by tianshenbio ▴ 130
1
vote
2
replies
835
views
Blast: use best hit or top20 hits?
blast blast2go GO annotation RNA-Seq
2.2 years ago by tianshenbio ▴ 130
0
votes
0
replies
531
views
How to specify -s option in RNAhybrid to predict miRNA targets?
miRNA rna-seq sequence RNAhybrid
2.2 years ago by tianshenbio ▴ 130
0
votes
1
reply
805
views
Comment: C: Compare expression level of isoforms among conditions - TPM or deseq2 normalised
2.2 years ago by tianshenbio ▴ 130
0
votes
3
replies
805
views
Compare expression level of isoforms among conditions - TPM or deseq2 normalised counts?
RNA-Seq deseq2 tximport salmon
2.2 years ago by tianshenbio ▴ 130
0
votes
0
replies
1.6k
views
Comment: C: How to subset the output of tximport in DE analysis using DEseq2
2.2 years ago by tianshenbio ▴ 130
0
votes
0
replies
1.6k
views
Comment: C: Correct gtf file format (AGAT toolkit)
2.2 years ago by tianshenbio ▴ 130
0
votes
4
replies
1.6k
views
Correct gtf file format (AGAT toolkit)
RNA-Seq gff gtf AGAT gff3
updated 2.2 years ago by 7.2k • written 2.2 years ago by ▴ 130
0
votes
0
replies
1.6k
views
Comment: C: Correct gtf file format (AGAT toolkit)
2.2 years ago by tianshenbio ▴ 130
0
votes
0
replies
2.2k
views
Comment: C: Why sortmerna 4.2.0 runs so slow?
2.2 years ago by tianshenbio ▴ 130
0
votes
0
replies
2.0k
views
Comment: C: Is Stringtie a suitable tool for both gene and transcript quantification?
2.2 years ago by tianshenbio ▴ 130
0
votes
0
replies
2.0k
views
Comment: C: Is Stringtie a suitable tool for both gene and transcript quantification?
2.2 years ago by tianshenbio ▴ 130
10
votes
5
replies
2.0k
views
Is Stringtie a suitable tool for both gene and transcript quantification?
stringtie RNA-Seq sequencing featurecounts gene
updated 7 weeks ago by • 0 • written 2.2 years ago by ▴ 130
0
votes
1
reply
1.4k
views
Comment: C: Read counts at gene and transcript level - hisat2+Featurecounts or Stringtie?+de
2.2 years ago by tianshenbio ▴ 130
1
vote
3
replies
1.4k
views
Read counts at gene and transcript level - hisat2+Featurecounts or Stringtie?+deseq2
RNA-Seq featurecounts stringtie hisat2 deseq2
2.2 years ago by tianshenbio ▴ 130
0
votes
0
replies
390
views
Comment: C: Proper design in deseq2
2.2 years ago by tianshenbio ▴ 130
2
votes
2
replies
390
views
Proper design in deseq2
RNA-Seq deseq2 gene R
updated 2.2 years ago by 12k • written 2.2 years ago by ▴ 130
1
vote
1
reply
2.5k
views
Filter out DE genes with low counts in deseq2
RNA-Seq R gene deseq2
updated 2.2 years ago by 64k • written 2.2 years ago by ▴ 130
0
votes
0
replies
870
views
Comment: C: Gffread_How to obtain fasta files of gene features (ORF, UTR) by transcripts bas
2.2 years ago by tianshenbio ▴ 130
0
votes
2
replies
870
views
Gffread_How to obtain fasta files of gene features (ORF, UTR) by transcripts based on gff?
RNA-Seq Assembly genome sequence gene
2.2 years ago by tianshenbio ▴ 130
4
votes
3
replies
821
views
How to extract sequence of a specific feature in gff
rna-seq gff genome assembly
updated 2.2 years ago by 7.2k • written 2.2 years ago by ▴ 130
0
votes
0
replies
997
views
Comment: C: After read mapping, count exons or genes?
2.2 years ago by tianshenbio ▴ 130
2
votes
2
replies
997
views
After read mapping, count exons or genes?
RNA-Seq featurecounts genome
updated 2.2 years ago by 64k • written 2.2 years ago by ▴ 130
0
votes
1
reply
470
views
Comment: C: Many paralogous genes in GO enrichment results
2.2 years ago by tianshenbio ▴ 130
0
votes
1
reply
470
views
Comment: C: Many paralogous genes in GO enrichment results
2.2 years ago by tianshenbio ▴ 130
0
votes
5
replies
470
views
Many paralogous genes in GO enrichment results
RNA-Seq GO enrichment gene
2.2 years ago by tianshenbio ▴ 130
0
votes
2
replies
1.3k
views
How to generate a dataframe of deseq2 result excluding 'low counts' and 'outliers' ?
deseq2 RNA-Seq
updated 2.2 years ago by 82k • written 2.2 years ago by ▴ 130
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