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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 81k • 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
440
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
0
replies
885
views
Comment: Comment: How to merge genomic features shared by more than one samples
2.9 years ago by tianshenbio ▴ 170
0
votes
1
reply
885
views
Comment: Comment: How to merge genomic features shared by more than one samples
3.0 years ago by tianshenbio ▴ 170
0
votes
4
replies
885
views
How to merge genomic features shared by more than one samples
bedtools gene RNA-seq bed annotation
2.9 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 3.0 years ago by 141k • written 3.0 years ago by ▴ 170
1
vote
0
replies
1.9k
views
Comment: Comment: How to select genes with multi-exon 3'UTR
3.0 years ago by tianshenbio ▴ 170
8
votes
6
replies
1.9k
views
How to select genes with multi-exon 3'UTR
rna-seq genome gff gene
updated 3.0 years ago by 8.5k • written 3.0 years ago by ▴ 170
1
vote
0
replies
2.7k
views
Functional annotation(GO,KEGG): Blast2GO+KAAS or EggNOG
blast2go eggnog kegg rna-seq genome
updated 3.1 years ago by 20 • written 4.0 years ago by ▴ 170
0
votes
1
reply
3.4k
views
Comment: C: Why sortmerna 4.2.0 runs so slow?
3.2 years ago by tianshenbio ▴ 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 2.5 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 4.0 years ago by ▴ 170
0
votes
0
replies
952
views
Comment: C: RNA-seq raw data lost
3.4 years ago by tianshenbio ▴ 170
3
votes
4
replies
952
views
RNA-seq raw data lost
RNA-Seq next-gen sequencing sequence
updated 3.4 years ago by 141k • written 3.4 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 3.8 years ago by ▴ 170
0
votes
0
replies
748
views
Comment: C: Can I directly blast mRNAs against nr database or I need to convert it to cds fi
3.7 years ago by tianshenbio ▴ 170
0
votes
0
replies
748
views
Comment: C: Can I directly blast mRNAs against nr database or I need to convert it to cds fi
3.7 years ago by tianshenbio ▴ 170
2
votes
4
replies
748
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
3.6k
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
3.4k
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
0
votes
0
replies
3.6k
views
Comment: C: How to visualise KEGG pathway?
3.8 years ago by tianshenbio ▴ 170
1
vote
2
replies
1.3k
views
Blast: use best hit or top20 hits?
blast blast2go GO annotation RNA-Seq
3.8 years ago by tianshenbio ▴ 170
0
votes
0
replies
814
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
1
reply
1.2k
views
Comment: C: Compare expression level of isoforms among conditions - TPM or deseq2 normalised
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
0
replies
2.7k
views
Comment: C: How to subset the output of tximport in DE analysis using DEseq2
3.9 years ago by tianshenbio ▴ 170
0
votes
0
replies
2.5k
views
Comment: C: Correct gtf file format (AGAT toolkit)
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
0
votes
0
replies
2.5k
views
Comment: C: Correct gtf file format (AGAT toolkit)
3.9 years ago by tianshenbio ▴ 170
0
votes
0
replies
3.4k
views
Comment: C: Why sortmerna 4.2.0 runs so slow?
3.9 years ago by tianshenbio ▴ 170
0
votes
0
replies
3.6k
views
Comment: C: Is Stringtie a suitable tool for both gene and transcript quantification?
3.9 years ago by tianshenbio ▴ 170
0
votes
0
replies
3.6k
views
Comment: C: Is Stringtie a suitable tool for both gene and transcript quantification?
3.9 years ago by tianshenbio ▴ 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
0
votes
1
reply
2.1k
views
Comment: C: Read counts at gene and transcript level - hisat2+Featurecounts or Stringtie?+de
3.9 years ago by tianshenbio ▴ 170
1
vote
3
replies
2.1k
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
0
votes
0
replies
626
views
Comment: C: Proper design in deseq2
3.9 years ago by tianshenbio ▴ 170
2
votes
2
replies
626
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 81k • written 3.9 years ago by ▴ 170
0
votes
0
replies
1.6k
views
Comment: C: Gffread_How to obtain fasta files of gene features (ORF, UTR) by transcripts bas
3.9 years ago by tianshenbio ▴ 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
0
votes
0
replies
1.7k
views
Comment: C: After read mapping, count exons or genes?
3.9 years ago by tianshenbio ▴ 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 81k • written 3.9 years ago by ▴ 170
0
votes
1
reply
772
views
Comment: C: Many paralogous genes in GO enrichment results
3.9 years ago by tianshenbio ▴ 170
0
votes
1
reply
772
views
Comment: C: Many paralogous genes in GO enrichment results
3.9 years ago by tianshenbio ▴ 170
0
votes
5
replies
772
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
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