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Showing :
questions
2
votes
5
replies
4.9k
views
About calculating the GC content in a sliding window
gccontent
bedtools
updated 22 months ago by
schlogl
▴ 160 • written 3.7 years ago by
jon.brate
▴ 310
3
votes
2
replies
1.5k
views
How to create alignment of UTR's for use in TargetScan?
mirna
targetscan
5.1 years ago by
jon.brate
▴ 310
1
vote
5
replies
2.5k
views
Trying to get access to the Trinity R commands...
Trinity
R
rna-seq
5.3 years ago by
jon.brate
▴ 310
0
votes
5
replies
2.4k
views
MaSuRCA failed to extract the best long reads
assembly
MaSuRCA
updated 5.9 years ago by
Kundan Kumar
• 0 • written 6.2 years ago by
jon.brate
▴ 310
9
votes
11
replies
4.2k
views
What is Trimmomatic -validatePairs, and how to use it?
trimmomatic
updated 5.9 years ago by
h.mon
35k • written 5.9 years ago by
jon.brate
▴ 310
1
vote
3
replies
1.1k
views
Bowtie2 mapping did not finish, can I still use the .sam file?
bowtie2
bowtie
updated 6.1 years ago by
WouterDeCoster
47k • written 6.1 years ago by
jon.brate
▴ 310
0
votes
0
replies
1.7k
views
Can I use Canu corrected reads without Can trim?
canu
assembly
smartdenovo
6.2 years ago by
jon.brate
▴ 310
17
votes
16
replies
14k
views
10 follow
How to extract the longest isoform from multi fasta file
perl
extract
fasta
python
isoform
updated 29 days ago by
Madeleine
• 0 • written 9.8 years ago by
jon.brate
▴ 310
2
votes
1
reply
1.2k
views
Does the order of sequences in a blast database matter?
blast
updated 7.6 years ago by
biotech
▴ 570 • written 7.6 years ago by
jon.brate
▴ 310
2
votes
2
replies
5.1k
views
How to get different colors on coverage tracks in IGV
IGV
RNA-Seq
updated 7.7 years ago by
Carlo Yague
8.7k • written 7.7 years ago by
jon.brate
▴ 310
29
votes
12
replies
15k
views
Is the Picard SortSam queryname or coordinate equivalent to samtools sort -n?
samtools
picard
sort
updated 8.1 years ago by
John
13k • written 9.9 years ago by
jon.brate
▴ 310
6
votes
15
replies
5.1k
views
coverageBed: what am I doing wrong?
bedtools
coverage
bam
updated 8.2 years ago by
Aaronquinlan
12k • written 8.2 years ago by
jon.brate
▴ 310
1
vote
3
replies
3.8k
views
How to define intergenic regions from cufflinks .gtf-file (separate introns from intergenic)
cufflinks
gtf
intergenic
updated 8.6 years ago by
Devon Ryan
104k • written 8.6 years ago by
jon.brate
▴ 310
2
votes
4
replies
5.3k
views
Is it possible (or does it make sense) to display two different gene sets in one PCA-plot?
deseq2
pca
clustering
RNA-Seq
updated 8.6 years ago by
Shicheng Guo
★ 9.4k • written 8.6 years ago by
jon.brate
▴ 310
1
vote
4
replies
2.7k
views
Does the order of input files matter when mapping paired-end strand specific RNA-seq reads?
mapping
RNA-Seq
tophat2
bowtie2
illumina
updated 9.0 years ago by
Devon Ryan
104k • written 9.0 years ago by
jon.brate
▴ 310
2
votes
1
reply
4.7k
views
Need advice: I want to display a heatmap of gene expression based on a dendrogram from the WGCNA package
heatmap
clustering
RNA-Seq
wgcna
R
updated 15 months ago by
Ram
43k • written 9.0 years ago by
jon.brate
▴ 310
13
votes
8
replies
3.6k
views
What is your preferred way to map cDNA sequences to genome?
mapping
alignment
blat
blast
gff
updated 22 months ago by
Ram
43k • written 9.0 years ago by
jon.brate
▴ 310
1
vote
6
replies
4.3k
views
Struggle to loop over multiple files with BioPython
python
loop
biopython
updated 22 months ago by
Ram
43k • written 9.0 years ago by
jon.brate
▴ 310
5
votes
11
replies
5.3k
views
How can I remove sequences with only gaps (-) from a multi-fasta file?
fasta
trimming
unix
updated 9.0 years ago by
Ram
43k • written 9.0 years ago by
jon.brate
▴ 310
9
votes
5
replies
4.9k
views
Make a .gmt file using bash for loop
bash
gmt
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
jon.brate
▴ 310
0
votes
1
reply
4.2k
views
How to write relaxed AND sequential Phylip format using AlignIO?
alignment
Phylip
AlignIO
updated 2.2 years ago by
Ram
43k • written 9.5 years ago by
jon.brate
▴ 310
2
votes
1
reply
2.2k
views
How to statistically test whether overlapping transcripts belong to separate genes or not
RNA-Seq
gene
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
jon.brate
▴ 310
3
votes
18
replies
6.4k
views
Split a concatenated alignment into individual gene alignments
alignment
phylogeny
nexus
concatenation
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
jon.brate
▴ 310
14
votes
8
replies
12k
views
Plot statistics from gtf/gff file
gtf
exons
annotation
gff
plot
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
jon.brate
▴ 310
14
votes
18
replies
10k
views
8 follow
Trim Poly-A Tail And Trailing Nucleotides
trimming
rna-seq
updated 10.2 years ago by
gammyknee
▴ 210 • written 10.2 years ago by
jon.brate
▴ 310
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