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521
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Comment: Comment: Different strandedness from HISAT2 and STAR alignment
3 months ago by tianshenbio ▴ 180
0
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0
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521
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Comment: Comment: Different strandedness from HISAT2 and STAR alignment
3 months ago by tianshenbio ▴ 180
0
votes
1
reply
521
views
Comment: Comment: Different strandedness from HISAT2 and STAR alignment
3 months ago by tianshenbio ▴ 180
2
votes
5
replies
521
views
Different strandedness from HISAT2 and STAR alignment
star strandedness RNA-seq alignment hisat2
3 months ago by tianshenbio ▴ 180
3
votes
7
replies
1.9k
views
Is removing rRNAs, tRNAs, etc really a necessary step in the miRNA analysis?
mirdeep2 miRNA RNA-seq
updated 23 months ago by ▴ 30 • written 3.6 years ago by ▴ 180
5
votes
4
replies
3.1k
views
How to subset the output of tximport in DE analysis using DEseq2
DEseq2 tximport rna-seq r
updated 2.9 years ago by 85k • written 4.5 years ago by ▴ 180
2
votes
12
replies
6.4k
views
How to get KEGG pathway names in KEGG enrichment analysis using clusterprofiler
annotation enrichment KEGG clusterprofiler RNA-Seq
updated 3.3 years ago by ★ 2.6k • written 4.6 years ago by ▴ 180
0
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0
replies
497
views
how to annotate mapping peaks within a defined genomic region？
piRNA genome RNA-seq annotation
3.5 years ago by tianshenbio ▴ 180
0
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0
replies
1.0k
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Comment: Comment: How to merge genomic features shared by more than one samples
3.6 years ago by tianshenbio ▴ 180
0
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1
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1.0k
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Comment: Comment: How to merge genomic features shared by more than one samples
3.6 years ago by tianshenbio ▴ 180
0
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4
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1.0k
views
How to merge genomic features shared by more than one samples
bedtools gene RNA-seq bed annotation
3.6 years ago by tianshenbio ▴ 180
0
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1
reply
1.2k
views
Convert a DNA sequence to MEME format
FIMO fasta motif MEME-suite format conversion
updated 3.6 years ago by 147k • written 3.6 years ago by ▴ 180
1
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0
replies
2.1k
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Comment: Comment: How to select genes with multi-exon 3'UTR
3.6 years ago by tianshenbio ▴ 180
8
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6
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2.1k
views
How to select genes with multi-exon 3'UTR
rna-seq genome gff gene
updated 3.6 years ago by 8.9k • written 3.7 years ago by ▴ 180
1
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0
replies
3.0k
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Functional annotation(GO,KEGG): Blast2GO+KAAS or EggNOG
blast2go eggnog kegg rna-seq genome
updated 3.8 years ago by 20 • written 4.6 years ago by ▴ 180
0
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1
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3.7k
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Comment: C: Why sortmerna 4.2.0 runs so slow?
3.8 years ago by tianshenbio ▴ 180
2
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8
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3.7k
views
Why sortmerna 4.2.0 runs so slow?
RNA-Seq sortmerna software error RNA rna-seq
updated 3.8 years ago by ▴ 20 • written 4.6 years ago by ▴ 180
2
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3
replies
5.5k
views
How to get a list of all KEGG ko terms vs names?
kegg annotation rna-seq
updated 3.1 years ago by ▴ 10 • written 4.6 years ago by ▴ 180
8
votes
12
replies
17k
views
6 follow
Clusterprofiler error: No gene can be mapped
RNA-seq GO enrichment R GO clusterProfiler
updated 3.6 years ago by ▴ 20 • written 4.6 years ago by ▴ 180
0
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0
replies
1.2k
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Comment: C: RNA-seq raw data lost
4.0 years ago by tianshenbio ▴ 180
3
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4
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1.2k
views
RNA-seq raw data lost
RNA-Seq next-gen sequencing sequence
updated 4.0 years ago by 147k • written 4.0 years ago by ▴ 180
4
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2
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2.5k
views
What would be the best strategy to merge the GO annotation from blast2go, InterProScan, and eggnog
interproscan eggnog blast2go GO RNA-Seq
updated 4.3 years ago by 20 • written 4.4 years ago by ▴ 180
0
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0
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831
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Comment: C: Can I directly blast mRNAs against nr database or I need to convert it to cds fi
4.3 years ago by tianshenbio ▴ 180
0
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0
replies
831
views
Comment: C: Can I directly blast mRNAs against nr database or I need to convert it to cds fi
4.3 years ago by tianshenbio ▴ 180
2
votes
4
replies
831
views
Can I directly blast mRNAs against nr database or I need to convert it to cds first
rna-seq annotation blast genome
updated 4.3 years ago by 13k • written 4.3 years ago by ▴ 180
3
votes
4
replies
4.4k
views
How to visualise KEGG pathway?
kegg enrichment RNA-Seq
updated 4.3 years ago by ▴ 440 • written 4.4 years ago by ▴ 180
1
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3
replies
4.2k
views
How do I remove certain sequences in fasta based on header?
fasta sequence RNA-Seq
updated 15 days ago by 15k • written 4.4 years ago by ▴ 180
0
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0
replies
4.4k
views
Comment: C: How to visualise KEGG pathway?
4.4 years ago by tianshenbio ▴ 180
1
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2
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1.4k
views
Blast: use best hit or top20 hits?
blast blast2go GO annotation RNA-Seq
4.4 years ago by tianshenbio ▴ 180
0
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0
replies
884
views
How to specify -s option in RNAhybrid to predict miRNA targets?
miRNA rna-seq sequence RNAhybrid
4.5 years ago by tianshenbio ▴ 180
0
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1
reply
1.4k
views
Comment: C: Compare expression level of isoforms among conditions - TPM or deseq2 normalised
4.5 years ago by tianshenbio ▴ 180
0
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3
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1.4k
views
Compare expression level of isoforms among conditions - TPM or deseq2 normalised counts?
RNA-Seq deseq2 tximport salmon
4.5 years ago by tianshenbio ▴ 180
0
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0
replies
3.1k
views
Comment: C: How to subset the output of tximport in DE analysis using DEseq2
4.5 years ago by tianshenbio ▴ 180
0
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0
replies
2.8k
views
Comment: C: Correct gtf file format (AGAT toolkit)
4.5 years ago by tianshenbio ▴ 180
0
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4
replies
2.8k
views
Correct gtf file format (AGAT toolkit)
RNA-Seq gff gtf AGAT gff3
updated 4.5 years ago by 8.9k • written 4.5 years ago by ▴ 180
0
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0
replies
2.8k
views
Comment: C: Correct gtf file format (AGAT toolkit)
4.5 years ago by tianshenbio ▴ 180
0
votes
0
replies
3.7k
views
Comment: C: Why sortmerna 4.2.0 runs so slow?
4.5 years ago by tianshenbio ▴ 180
0
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0
replies
4.4k
views
Comment: C: Is Stringtie a suitable tool for both gene and transcript quantification?
4.5 years ago by tianshenbio ▴ 180
0
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0
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4.4k
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Comment: C: Is Stringtie a suitable tool for both gene and transcript quantification?
4.5 years ago by tianshenbio ▴ 180
10
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5
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4.4k
views
Is Stringtie a suitable tool for both gene and transcript quantification?
stringtie RNA-Seq sequencing featurecounts gene
updated 2.4 years ago by • 0 • written 4.5 years ago by ▴ 180
0
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1
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2.4k
views
Comment: C: Read counts at gene and transcript level - hisat2+Featurecounts or Stringtie?+de
4.5 years ago by tianshenbio ▴ 180
1
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3
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2.4k
views
Read counts at gene and transcript level - hisat2+Featurecounts or Stringtie?+deseq2
RNA-Seq featurecounts stringtie hisat2 deseq2
4.5 years ago by tianshenbio ▴ 180
0
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0
replies
710
views
Comment: C: Proper design in deseq2
4.5 years ago by tianshenbio ▴ 180
2
votes
2
replies
710
views
Proper design in deseq2
RNA-Seq deseq2 gene R
updated 4.5 years ago by 14k • written 4.5 years ago by ▴ 180
1
vote
1
reply
3.6k
views
Filter out DE genes with low counts in deseq2
RNA-Seq R gene deseq2
updated 4.5 years ago by 85k • written 4.5 years ago by ▴ 180
0
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0
replies
1.8k
views
Comment: C: Gffread_How to obtain fasta files of gene features (ORF, UTR) by transcripts bas
4.5 years ago by tianshenbio ▴ 180
0
votes
2
replies
1.8k
views
Gffread_How to obtain fasta files of gene features (ORF, UTR) by transcripts based on gff?
RNA-Seq Assembly genome sequence gene
4.5 years ago by tianshenbio ▴ 180
4
votes
3
replies
1.9k
views
How to extract sequence of a specific feature in gff
rna-seq gff genome assembly
updated 4.5 years ago by 8.9k • written 4.5 years ago by ▴ 180
0
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0
replies
2.1k
views
Comment: C: After read mapping, count exons or genes?
4.5 years ago by tianshenbio ▴ 180
6
votes
2
replies
2.1k
views
After read mapping, count exons or genes?
RNA-Seq featurecounts genome
updated 4.5 years ago by 85k • written 4.5 years ago by ▴ 180
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