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GFF problem - gtf_to_fasta (Tophat) outputs only 2 sequences from 70 entries in GFF?
tophat RNA-Seq GFF GTF
updated 3.8 years ago by 20 • written 8.9 years ago by ▴ 150
0
votes
5
replies
1.1k
views
pathway or network from DEG list tool (plant)
DEG network pathway
updated 3.8 years ago by ★ 1.3k • written 3.8 years ago by ▴ 150
10
votes
12
replies
8.0k
views
8 follow
Qiime file for Krona pie chart?
qiime krona
updated 4.2 years ago by ▴ 20 • written 8.0 years ago by ▴ 150
2
votes
8
replies
1.5k
views
Collapsing BAM based on seq and positions
bam collapse
4.2 years ago by manekineko ▴ 150
18
votes
14
replies
6.3k
views
8 follow
Extending ends of sequences with the help of reads?
Assembly
updated 16 months ago by 43k • written 8.9 years ago by ▴ 150
0
votes
0
replies
959
views
qiime open vs closed picking with SILVA?
qiime silva
4.7 years ago by manekineko ▴ 150
0
votes
1
reply
2.7k
views
RDP classifier pipeline question (16s analysis)
16s
updated 6.2 years ago by ★ 2.2k • written 7.3 years ago by ▴ 150
2
votes
7
replies
2.5k
views
LoFreq outputing no SNP?
LoFreq
updated 6.3 years ago by 20 • written 6.4 years ago by ▴ 150
2
votes
3
replies
1.2k
views
Help downloading pepper genome (I have bad speed connection)
pepper capsicum genome
6.5 years ago by manekineko ▴ 150
0
votes
1
reply
1.4k
views
16s analysis MySeq PE - analysis of only forward reads?
16s metagenomics
updated 6.5 years ago by 10k • written 6.5 years ago by ▴ 150
1
vote
9
replies
1.9k
views
Uncollapsing FASTA file
uncollapsing
updated 6.5 years ago by 21k • written 6.5 years ago by ▴ 150
3
votes
7
replies
2.8k
views
Very slow Bio-linux on VirtualBox?
bio-linux virtualbox ova
updated 7.8 years ago by ★ 4.0k • written 8.0 years ago by ▴ 150
2
votes
1
reply
1.7k
views
Statistics and visualization software (STAMP similar) for general purposes?
stamp statistics visualization
updated 7.8 years ago by 20 • written 8.0 years ago by ▴ 150
0
votes
1
reply
2.8k
views
Edit BIOM file - delete samples, rearrange samples?
biom
updated 7.9 years ago by ▴ 730 • written 7.9 years ago by ▴ 150
1
vote
3
replies
3.1k
views
16s amplicon metagenomics - no mapping file?
mothur qiime
updated 8.0 years ago by ▴ 870 • written 8.0 years ago by ▴ 150
5
votes
9
replies
4.3k
views
htseq-count not working with miRbase gff?
htseq-count mirbase gff
updated 18 months ago by 43k • written 8.8 years ago by ▴ 150
6
votes
4
replies
2.6k
views
Statistical question (Deseq, Cuffdis) when one condition is zero?
differential expression statistics
updated 8.7 years ago by 14k • written 8.8 years ago by ▴ 150
1
vote
13
replies
2.6k
views
Strange mapping on miRNAs from RNA-seq library
miRNA RNA-seq
updated 18 months ago by 43k • written 8.8 years ago by ▴ 150
3
votes
3
replies
2.2k
views
Cuffdiff results transcript testing
cuffdiff RNA-seq
updated 18 months ago by 43k • written 8.8 years ago by ▴ 150
0
votes
9
replies
2.2k
views
Tophat mapping less reads (and less properly paired) when more real -r is specified?
tophat RNA-Seq
updated 18 months ago by 43k • written 8.8 years ago by ▴ 150
3
votes
3
replies
5.1k
views
Mean insert size and Mean inner distance between mate pairs
RNA-Seq
updated 18 months ago by 43k • written 8.8 years ago by ▴ 150
2
votes
5
replies
2.5k
views
Check is RNA-seq mapping (tophat) is performed ok (hg38)?
tophat RNA-Seq
updated 18 months ago by 43k • written 8.8 years ago by ▴ 150
6
votes
6
replies
4.4k
views
Very short reads (20-22) , bowtie and tophat not doing gapped alignment
RNA-Seq
updated 18 months ago by 43k • written 8.9 years ago by ▴ 150
1
vote
5
replies
4.9k
views
Problems with STAR mapping output
RNA-Seq STAR
updated 16 months ago by 43k • written 8.9 years ago by ▴ 150
2
votes
6
replies
6.2k
views
multiple paired-end files for one sample?
RNA-Seq
updated 18 months ago by 43k • written 8.8 years ago by ▴ 150
0
votes
2
replies
1.6k
views
miRNAs differential expression with no replicates
mirna
updated 17 months ago by 43k • written 8.8 years ago by ▴ 150
0
votes
4
replies
4.5k
views
Deseq web-based (with GUI)
RNA-Seq
updated 17 months ago by 43k • written 8.8 years ago by ▴ 150
3
votes
4
replies
3.5k
views
bowtie options for exact match with reference short sequence
bowtie exact option
updated 17 months ago by 43k • written 8.8 years ago by ▴ 150
0
votes
6
replies
7.2k
views
Removing barcode and adapters?
sequencing adapters
updated 17 months ago by 43k • written 8.8 years ago by ▴ 150
2
votes
4
replies
2.3k
views
htseq-count counts all reads as no_feature
htseq-count
updated 16 months ago by 43k • written 8.9 years ago by ▴ 150
2
votes
4
replies
1.2k
views
Way to check if there is local trimmed alihned reads BOWTIE2
bowtie2
updated 16 months ago by 43k • written 8.9 years ago by ▴ 150
0
votes
1
reply
1.9k
views
GFF model in Tophat and/or Cufflinks?
RNA-Seq
updated 8.9 years ago by ★ 2.2k • written 8.9 years ago by ▴ 150
7
votes
10
replies
3.7k
views
Count number of mapped raw reads for each transcript in SAM file
RNA-Seq
updated 16 months ago by 43k • written 8.9 years ago by ▴ 150
4
votes
12
replies
2.1k
views
Tool to retrieve regions with reads?
RNA-Seq
updated 16 months ago by 43k • written 8.9 years ago by ▴ 150
2
votes
1
reply
1.8k
views
smallRNA-seq, but have files R1/R1fastq?
fastq smallRNAs single-end
updated 15 months ago by 43k • written 9.0 years ago by ▴ 150
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