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Comment: Comment: Different strandedness from HISAT2 and STAR alignment
13 months ago by tianshenbio ▴ 190
0
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0
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1.3k
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Comment: Comment: Different strandedness from HISAT2 and STAR alignment
13 months ago by tianshenbio ▴ 190
0
votes
1
reply
1.3k
views
Comment: Comment: Different strandedness from HISAT2 and STAR alignment
13 months ago by tianshenbio ▴ 190
2
votes
5
replies
1.3k
views
Different strandedness from HISAT2 and STAR alignment
star strandedness RNA-seq alignment hisat2
13 months ago by tianshenbio ▴ 190
3
votes
7
replies
2.5k
views
Is removing rRNAs, tRNAs, etc really a necessary step in the miRNA analysis?
mirdeep2 miRNA RNA-seq
updated 2.7 years ago by ▴ 30 • written 4.4 years ago by ▴ 190
5
votes
4
replies
3.7k
views
How to subset the output of tximport in DE analysis using DEseq2
DEseq2 tximport rna-seq r
updated 3.7 years ago by 89k • written 5.3 years ago by ▴ 190
2
votes
12
replies
7.8k
views
How to get KEGG pathway names in KEGG enrichment analysis using clusterprofiler
annotation enrichment KEGG clusterprofiler RNA-Seq
updated 4.1 years ago by ★ 2.6k • written 5.4 years ago by ▴ 190
0
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0
replies
603
views
how to annotate mapping peaks within a defined genomic region？
piRNA genome RNA-seq annotation
4.3 years ago by tianshenbio ▴ 190
0
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0
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1.3k
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Comment: Comment: How to merge genomic features shared by more than one samples
4.4 years ago by tianshenbio ▴ 190
0
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1
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1.3k
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Comment: Comment: How to merge genomic features shared by more than one samples
4.4 years ago by tianshenbio ▴ 190
0
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4
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1.3k
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How to merge genomic features shared by more than one samples
bedtools gene RNA-seq bed annotation
4.4 years ago by tianshenbio ▴ 190
0
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1
reply
1.5k
views
Convert a DNA sequence to MEME format
FIMO fasta motif MEME-suite format conversion
updated 4.5 years ago by 154k • written 4.5 years ago by ▴ 190
1
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0
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2.6k
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Comment: Comment: How to select genes with multi-exon 3'UTR
4.5 years ago by tianshenbio ▴ 190
8
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6
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2.6k
views
How to select genes with multi-exon 3'UTR
rna-seq genome gff gene
updated 4.5 years ago by 9.3k • written 4.5 years ago by ▴ 190
1
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0
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3.5k
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Functional annotation(GO,KEGG): Blast2GO+KAAS or EggNOG
blast2go eggnog kegg rna-seq genome
updated 4.6 years ago by 20 • written 5.5 years ago by ▴ 190
0
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1
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4.4k
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Comment: C: Why sortmerna 4.2.0 runs so slow?
4.6 years ago by tianshenbio ▴ 190
2
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8
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4.4k
views
Why sortmerna 4.2.0 runs so slow?
RNA-Seq sortmerna software error RNA rna-seq
updated 4.6 years ago by ▴ 20 • written 5.4 years ago by ▴ 190
2
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3
replies
8.7k
views
How to get a list of all KEGG ko terms vs names?
kegg annotation rna-seq
updated 4.0 years ago by ▴ 10 • written 5.5 years ago by ▴ 190
8
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12
replies
19k
views
6 follow
Clusterprofiler error: No gene can be mapped
RNA-seq GO enrichment R GO clusterProfiler
updated 4.4 years ago by ▴ 20 • written 5.5 years ago by ▴ 190
0
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0
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1.6k
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Comment: C: RNA-seq raw data lost
4.9 years ago by tianshenbio ▴ 190
3
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4
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1.6k
views
RNA-seq raw data lost
RNA-Seq next-gen sequencing sequence
updated 4.9 years ago by 154k • written 4.9 years ago by ▴ 190
4
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2
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2.9k
views
What would be the best strategy to merge the GO annotation from blast2go, InterProScan, and eggnog
interproscan eggnog blast2go GO RNA-Seq
updated 5.1 years ago by 20 • written 5.3 years ago by ▴ 190
0
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0
replies
1.1k
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Comment: C: Can I directly blast mRNAs against nr database or I need to convert it to cds fi
5.1 years ago by tianshenbio ▴ 190
0
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0
replies
1.1k
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Comment: C: Can I directly blast mRNAs against nr database or I need to convert it to cds fi
5.1 years ago by tianshenbio ▴ 190
2
votes
4
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1.1k
views
Can I directly blast mRNAs against nr database or I need to convert it to cds first
rna-seq annotation blast genome
updated 5.1 years ago by 13k • written 5.1 years ago by ▴ 190
3
votes
4
replies
5.7k
views
How to visualise KEGG pathway?
kegg enrichment RNA-Seq
updated 5.1 years ago by ▴ 440 • written 5.3 years ago by ▴ 190
1
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3
replies
5.3k
views
How do I remove certain sequences in fasta based on header?
fasta sequence RNA-Seq
updated 10 months ago by 15k • written 5.2 years ago by ▴ 190
0
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0
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5.7k
views
Comment: C: How to visualise KEGG pathway?
5.3 years ago by tianshenbio ▴ 190
1
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2
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1.7k
views
Blast: use best hit or top20 hits?
blast blast2go GO annotation RNA-Seq
5.3 years ago by tianshenbio ▴ 190
0
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0
replies
1.1k
views
How to specify -s option in RNAhybrid to predict miRNA targets?
miRNA rna-seq sequence RNAhybrid
5.3 years ago by tianshenbio ▴ 190
0
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1
reply
1.7k
views
Comment: C: Compare expression level of isoforms among conditions - TPM or deseq2 normalised
5.3 years ago by tianshenbio ▴ 190
0
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3
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1.7k
views
Compare expression level of isoforms among conditions - TPM or deseq2 normalised counts?
RNA-Seq deseq2 tximport salmon
5.3 years ago by tianshenbio ▴ 190
0
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0
replies
3.7k
views
Comment: C: How to subset the output of tximport in DE analysis using DEseq2
5.3 years ago by tianshenbio ▴ 190
0
votes
0
replies
3.4k
views
Comment: C: Correct gtf file format (AGAT toolkit)
5.3 years ago by tianshenbio ▴ 190
0
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4
replies
3.4k
views
Correct gtf file format (AGAT toolkit)
RNA-Seq gff gtf AGAT gff3
updated 5.3 years ago by 9.3k • written 5.3 years ago by ▴ 190
0
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0
replies
3.4k
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Comment: C: Correct gtf file format (AGAT toolkit)
5.3 years ago by tianshenbio ▴ 190
0
votes
0
replies
4.4k
views
Comment: C: Why sortmerna 4.2.0 runs so slow?
5.3 years ago by tianshenbio ▴ 190
0
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0
replies
5.6k
views
Comment: C: Is Stringtie a suitable tool for both gene and transcript quantification?
5.3 years ago by tianshenbio ▴ 190
0
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0
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5.6k
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Comment: C: Is Stringtie a suitable tool for both gene and transcript quantification?
5.3 years ago by tianshenbio ▴ 190
10
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5
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5.6k
views
Is Stringtie a suitable tool for both gene and transcript quantification?
stringtie RNA-Seq sequencing featurecounts gene
updated 3.2 years ago by • 0 • written 5.3 years ago by ▴ 190
0
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1
reply
2.7k
views
Comment: C: Read counts at gene and transcript level - hisat2+Featurecounts or Stringtie?+de
5.3 years ago by tianshenbio ▴ 190
1
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3
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2.7k
views
Read counts at gene and transcript level - hisat2+Featurecounts or Stringtie?+deseq2
RNA-Seq featurecounts stringtie hisat2 deseq2
5.3 years ago by tianshenbio ▴ 190
0
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0
replies
940
views
Comment: C: Proper design in deseq2
5.3 years ago by tianshenbio ▴ 190
2
votes
2
replies
940
views
Proper design in deseq2
RNA-Seq deseq2 gene R
updated 5.3 years ago by 15k • written 5.3 years ago by ▴ 190
1
vote
1
reply
4.0k
views
Filter out DE genes with low counts in deseq2
RNA-Seq R gene deseq2
updated 5.3 years ago by 89k • written 5.3 years ago by ▴ 190
0
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0
replies
2.1k
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Comment: C: Gffread_How to obtain fasta files of gene features (ORF, UTR) by transcripts bas
5.3 years ago by tianshenbio ▴ 190
0
votes
2
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2.1k
views
Gffread_How to obtain fasta files of gene features (ORF, UTR) by transcripts based on gff?
RNA-Seq Assembly genome sequence gene
5.3 years ago by tianshenbio ▴ 190
4
votes
3
replies
2.2k
views
How to extract sequence of a specific feature in gff
rna-seq gff genome assembly
updated 5.3 years ago by 9.3k • written 5.3 years ago by ▴ 190
0
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0
replies
2.5k
views
Comment: C: After read mapping, count exons or genes?
5.3 years ago by tianshenbio ▴ 190
6
votes
2
replies
2.5k
views
After read mapping, count exons or genes?
RNA-Seq featurecounts genome
updated 5.3 years ago by 89k • written 5.3 years ago by ▴ 190
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