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Showing :
questions
4
votes
11
replies
6.4k
views
8 follow
Filtering out the spliced reads from bam file.
RNA-Seq
BAM
spliced-reads
updated 17 months ago by
barslmn
★ 2.1k • written 7.9 years ago by
EVR
▴ 610
0
votes
0
replies
562
views
Genomic intervals to transcriptomic intervals
RNA-Seq
bed
4.0 years ago by
EVR
▴ 610
2
votes
1
reply
667
views
Statistically overrepresented gene types from Differentially expressed genes.
RNA-Seq
next-gen
gene-types
enrichment
updated 4.2 years ago by
i.sudbery
19k • written 4.2 years ago by
EVR
▴ 610
0
votes
2
replies
1.5k
views
LRT test in DESeq2 gives weird volcano plot
DEseq2
LRT
RNA-Seq
VolcanoPlot
updated 4.7 years ago by
ATpoint
82k • written 4.7 years ago by
EVR
▴ 610
3
votes
12
replies
4.1k
views
Counting mutated reads from RNA Seq data
Mutation
Variant-analysis
RNA-Seq
Samtools
updated 19 months ago by
Ram
43k • written 8.8 years ago by
EVR
▴ 610
3
votes
3
replies
2.8k
views
Identifying miRNA, RNA-binding sites in UTRs
UTRs
miNRA
RNA-binding protein
updated 6.5 years ago by
Russ
▴ 500 • written 6.5 years ago by
EVR
▴ 610
0
votes
4
replies
5.1k
views
Tool for predicting RNA binding protein
RNA-Seq
RNA-binding-proteins
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
EVR
▴ 610
0
votes
3
replies
1.9k
views
Merging bed intervals within a group
Bedtools
bedops
BED
6.7 years ago by
EVR
▴ 610
5
votes
10
replies
2.9k
views
6 follow
Average intron length in Drosophila melagnoster
Drosophila
Intron_length
updated 6.7 years ago by
Malcolm.Cook
★ 1.5k • written 6.7 years ago by
EVR
▴ 610
2
votes
5
replies
3.2k
views
IGV error: Error loading SAM header: For sequence 34711, text and binary have different lengths in file.
RNA-Seq
BAM
IGV
updated 6.8 years ago by
dyollluap
▴ 310 • written 6.8 years ago by
EVR
▴ 610
0
votes
3
replies
1.5k
views
Finding fragemented transcriptome
transcriptome
denovo_assembly
updated 6.9 years ago by
Rohit
★ 1.5k • written 6.9 years ago by
EVR
▴ 610
1
vote
1
reply
2.0k
views
Splitting the Spliced reads from genome Alignment
bed
bedtools
bedops
bam
Spliced_reads
7.0 years ago by
EVR
▴ 610
3
votes
3
replies
2.6k
views
Indpendent Filtering in DESeq2
DESeq2
Independent filtering
updated 7.2 years ago by
Devon Ryan
104k • written 7.2 years ago by
EVR
▴ 610
5
votes
6
replies
2.0k
views
Pairwise comparision in DESeq2
RNA-Seq
DESeq2
updated 7.2 years ago by
Carlo Yague
8.7k • written 7.2 years ago by
EVR
▴ 610
7
votes
8
replies
3.2k
views
Finding Batch effects in RNAseq data
RNA-Seq
batch-effect
7.2 years ago by
EVR
▴ 610
0
votes
2
replies
1.9k
views
Aligning reads to genome/transcriptome
RNA-Seq
Tophat2
bowtie2
bowtie
7.3 years ago by
EVR
▴ 610
4
votes
6
replies
5.0k
views
Extracting entries from GTF file
GTF
bed
updated 7.3 years ago by
Alex Reynolds
35k • written 7.3 years ago by
EVR
▴ 610
0
votes
2
replies
2.4k
views
DESeq2 Normalization of time course
DESeq2
RNA-Seq
Normalization
updated 7.3 years ago by
bioinfo17
▴ 30 • written 7.4 years ago by
EVR
▴ 610
4
votes
3
replies
8.9k
views
What is a "draft genome assembly"?
Genome_assembly
de novo
updated 7.5 years ago by
Damian Kao
16k • written 7.5 years ago by
EVR
▴ 610
0
votes
3
replies
1.6k
views
Computing intron length per trancript
intron_length
GFF3
7.5 years ago by
EVR
▴ 610
1
vote
6
replies
1.3k
views
Counting read orientation between ranges in a bed file
BED
bedtools
bedops
updated 7.6 years ago by
GouthamAtla
12k • written 7.6 years ago by
EVR
▴ 610
2
votes
2
replies
3.8k
views
Adding GO:IDs to the BLAST hits
Gene Ontology
BLAST
updated 7.6 years ago by
Mahmut Uludag
▴ 20 • written 7.6 years ago by
EVR
▴ 610
0
votes
4
replies
5.5k
views
Getting BP, MF and CC from GO IDs
Gene Ontology
updated 7.6 years ago by
EagleEye
7.5k • written 7.6 years ago by
EVR
▴ 610
1
vote
14
replies
2.2k
views
Compairng multiple sequence and finding similarity.
DNA_Sequences
Fasta
Sequence_comparision
updated 7.7 years ago by
GouthamAtla
12k • written 7.7 years ago by
EVR
▴ 610
2
votes
4
replies
2.1k
views
Finding alignment score for multi-read frombam/sam file
RNA-Seq
Bam
Sam
Tophat
Multi-read
7.8 years ago by
EVR
▴ 610
5
votes
3
replies
2.1k
views
Appending sequences in fasta file with identical headers
fasta
updated 7.8 years ago by
venu
7.1k • written 7.8 years ago by
EVR
▴ 610
1
vote
7
replies
1.8k
views
Extracting reads outside the boundaries in a BED file
bed_file
bedtools
updated 7.8 years ago by
Alex Reynolds
35k • written 7.8 years ago by
EVR
▴ 610
0
votes
1
reply
2.2k
views
Minimum and maximum Intron length of Oryza sativa
Intron length
Oryza sativa
tophat2
7.8 years ago by
EVR
▴ 610
0
votes
5
replies
2.1k
views
Oryza Sativa Transcriptome
Transcriptome
Oryza_sativa
updated 7.8 years ago by
Denise CS
★ 5.2k • written 7.8 years ago by
EVR
▴ 610
2
votes
4
replies
2.3k
views
Q33 in fastx_clipper
Fastx
RNA-Seq
updated 16 months ago by
Ram
43k • written 8.9 years ago by
EVR
▴ 610
2
votes
5
replies
1.7k
views
Evaluating the Genome aseemblies
RNA-Seq
genome
N50
updated 7.9 years ago by
igor
13k • written 7.9 years ago by
EVR
▴ 610
3
votes
5
replies
9.1k
views
Finding overlapping ranges in R
RNA-Seq
R
Overlapping-ranges
updated 7.9 years ago by
poisonAlien
★ 3.2k • written 7.9 years ago by
EVR
▴ 610
0
votes
0
replies
1.1k
views
Finidng the closest features near transcript boundaries in genome
RNA-Seq
bedtools
bedops
joining-features
8.0 years ago by
EVR
▴ 610
0
votes
4
replies
3.0k
views
Extracing the regions outside the target(transctip) region in genome
RNA-Seq
bedtools
samtools
bam_file
genome
updated 8.0 years ago by
Biostar
20 • written 8.1 years ago by
EVR
▴ 610
2
votes
3
replies
2.1k
views
Reading bam files and extratcing transcript from abm files in R
RNA-Seq
bam
samtools
updated 8.0 years ago by
GouthamAtla
12k • written 8.0 years ago by
EVR
▴ 610
0
votes
4
replies
2.1k
views
Detecting the peaks from RNAseq data
RNA-Seq
peak
bam
updated 8.0 years ago by
ivivek_ngs
★ 5.2k • written 8.0 years ago by
EVR
▴ 610
1
vote
4
replies
923
views
Mappping read to its exact postion in genome
RNA-Seq
TOPHAT
updated 8.0 years ago by
Devon Ryan
104k • written 8.0 years ago by
EVR
▴ 610
0
votes
1
reply
1.2k
views
Computing Genome Duplication
genome
Duplication
RNA-Seq
8.0 years ago by
EVR
▴ 610
0
votes
5
replies
2.8k
views
Counting reads within regions of interest
bam
RNA-Seq
coverage
8.1 years ago by
EVR
▴ 610
0
votes
4
replies
1.7k
views
Counting reads on genome
RNA-Seq
genome
transcriptome
updated 8.1 years ago by
mastal511
★ 2.1k • written 8.1 years ago by
EVR
▴ 610
3
votes
6
replies
2.5k
views
Identifying full length transcripts in a transcriptome
de-novo-Transcriptome
full-length-transcripts
updated 21 months ago by
Ram
43k • written 8.3 years ago by
EVR
▴ 610
1
vote
5
replies
3.0k
views
Aligning reads to genome together with transcriptome
RNA-Seq
Genome
Transcriptome
alignment
updated 22 months ago by
Ram
43k • written 8.2 years ago by
EVR
▴ 610
1
vote
1
reply
4.3k
views
Generating GTF file for de novo assmebled transcriptome
GTF
Transcriptome
updated 8.4 years ago by
Benn
8.3k • written 8.4 years ago by
EVR
▴ 610
0
votes
4
replies
6.4k
views
Log2 fold change heatmap
Log2foldchange
heatmap
Microarray
updated 21 months ago by
Ram
43k • written 8.4 years ago by
EVR
▴ 610
1
vote
1
reply
2.5k
views
Quality control for AB Solid fastq files
Fastqc
AB-Solid
RNA-Seq
updated 20 months ago by
Ram
43k • written 8.6 years ago by
EVR
▴ 610
13
votes
10
replies
9.8k
views
Finding the iIllumina index read from raw fastq file
RNA-Seq
illumina
index-read
updated 20 months ago by
Ram
43k • written 8.6 years ago by
EVR
▴ 610
0
votes
1
reply
2.3k
views
All reads deposited in Undetermined indices
RNA-Seq
demultiplexing
Undetermined_indices
updated 20 months ago by
Ram
43k • written 8.6 years ago by
EVR
▴ 610
2
votes
2
replies
3.1k
views
GO enrichment analysis on Non-model Organism
Enrichment-analysis
Gene-Ontology
updated 20 months ago by
Ram
43k • written 8.7 years ago by
EVR
▴ 610
1
vote
1
reply
2.0k
views
calculating the coverage percentage from blast8
Coverage percentage
blast8 output
blat
updated 8.7 years ago by
Biostar
20 • written 8.8 years ago by
EVR
▴ 610
0
votes
2
replies
1.9k
views
Extracting aligned consensus sequences for every transcript from sam file
RNA-Seq
sequence
bowtie-2
8.8 years ago by
EVR
▴ 610
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